DPpackage: Bayesian Semi- and Nonparametric Modeling in R

Data analysis sometimes requires the relaxation of parametric assumptions in order to gain modeling flexibility and robustness against mis-specification of the probability model. In the Bayesian context, this is accomplished by placing a prior distribution on a function space, such as the space of all probability distributions or the space of all regression functions. Unfortunately, posterior distributions ranging over function spaces are highly complex and hence sampling methods play a key role. This paper provides an introduction to a simple, yet comprehensive, set of programs for the implementation of some Bayesian nonparametric and semiparametric models in R, DPpackage. Currently, DPpackage includes models for marginal and conditional density estimation, receiver operating characteristic curve analysis, interval-censored data, binary regression data, item response data, longitudinal and clustered data using generalized linear mixed models, and regression data using generalized additive models. The package also contains functions to compute pseudo-Bayes factors for model comparison and for eliciting the precision parameter of the Dirichlet process prior, and a general purpose Metropolis sampling algorithm. To maximize computational efficiency, the actual sampling for each model is carried out using compiled C, C++ or Fortran code.

A Stochastic Frontier Model for Discrete Ordinal Outcomes: A Health Production Function

The stochastic frontier model used for continuous dependent variables is extended to accommodate output measured as a discrete ordinal outcome variable. Conditional on the inefficiency error, the assumptions of the ordered probit model are adopted for the log of output. Bayesian estimation utilizing a Gibbs sampler with data augmentation is applied to a convenient re-parameterisation of the model. Using panel data from an Australian longitudinal survey, demographic and socioeconomic characteristics are specified as inputs to health production, whereas production efficiency is made dependent on lifestyle factors. Posterior summary statistics are obtained for selected health status probabilities, efficiencies, and marginal effects.Bayesian estimation, Gibbs sampling, ordered probit, production efficiency.

Selling Goods of Unknown Quality: Forward versus Spot Auctions

We consider an environment where the sale can take place so early that both the seller and the potential buyers have the same uncertainty about the quality of the good. We present a simple model that allows the seller to put the good for sale before or after this uncertainty is resolved, , namely via forward auction or spot auction, respectively. We solve for the equilibrium of these two auctions and then compare the resulting revenues. We also consider the revenue implications of the insurance in forward auctions.Forward Trading, Forward Auctions, Spot Auctions

The R Package JMbayes for Fitting Joint Models for Longitudinal and Time-to-Event Data using MCMC

Joint models for longitudinal and time-to-event data constitute an attractive modeling framework that has received a lot of interest in the recent years. This paper presents the capabilities of the R package JMbayes for fitting these models under a Bayesian approach using Markon chain Monte Carlo algorithms. JMbayes can fit a wide range of joint models, including among others joint models for continuous and categorical longitudinal responses, and provides several options for modeling the association structure between the two outcomes. In addition, this package can be used to derive dynamic predictions for both outcomes, and offers several tools to validate these predictions in terms of discrimination and calibration. All these features are illustrated using a real data example on patients with primary biliary cirrhosis.Comment: 42 pages, 6 figure

Multivariate emulation of computer simulators: model selection and diagnostics with application to a humanitarian relief model

We present a common framework for Bayesian emulation methodologies for multivariate-output simulators, or computer models, that employ either parametric linear models or nonparametric Gaussian processes. Novel diagnostics suitable for multivariate covariance-separable emulators are developed and techniques to improve the adequacy of an emulator are discussed and implemented. A variety of emulators are compared for a humanitarian relief simulator, modelling aid missions to Sicily after a volcanic eruption and earthquake, and a sensitivity analysis is conducted to determine the sensitivity of the simulator output to changes in the input variables. The results from parametric and nonparametric emulators are compared in terms of prediction accuracy, uncertainty quantification and scientific interpretability