Biometrika - Advance Access

A negative binomial model for time series of counts

Davis, R. A., Wu, R. — 2009-07-01

We study generalized linear models for time series of counts, where serial dependence is introduced through a dependent latent process in the link function. Conditional on the covariates and the latent process, the observation is modelled by a negative binomial distribution. To estimate the regression coefficients, we maximize the pseudolikelihood that is based on a generalized linear model with the latent process suppressed. We show the consistency and asymptotic normality of the generalized linear model estimator when the latent process is a stationary strongly mixing process. We extend the asymptotic results to generalized linear models for time series, where the observation variable, conditional on covariates and a latent process, is assumed to have a distribution from a one-parameter exponential family. Thus, we unify in a common framework the results for Poisson log-linear regression models of Davis et al. (2000), negative binomial logit regression models and other similarly specified generalized linear models.

Improving point and interval estimators of monotone functions by rearrangement

Chernozhukov, V., Fernandez-Val, I., Galichon, A. — 2009-06-30

Suppose that a target function is monotonic and an available original estimate of this target function is not monotonic. Rearrangements, univariate and multivariate, transform the original estimate to a monotonic estimate that always lies closer in common metrics to the target function. Furthermore, suppose an original confidence interval, which covers the target function with probability at least 1-, is defined by an upper and lower endpoint functions that are not monotonic. Then the rearranged confidence interval, defined by the rearranged upper and lower endpoint functions, is monotonic, shorter in length in common norms than the original interval, and covers the target function with probability at least 1-. We illustrate the results with a growth chart example.

Gaussian process emulation of dynamic computer codes

Conti, S., Gosling, J. P., Oakley, J. E., O'hagan, A. — 2009-06-30

Computer codes are used in scientific research to study and predict the behaviour of complex systems. Their run times often make uncertainty and sensitivity analyses impractical because of the thousands of runs that are conventionally required, so efficient techniques have been developed based on a statistical representation of the code. The approach is less straightforward for dynamic codes, which represent time-evolving systems. We develop a novel iterative system to build a statistical model of dynamic computer codes, which is demonstrated on a rainfall-runoff simulator.

Empirical Bayes estimation for additive hazards regression models

Sinha, D., McHenry, M. B., Lipsitz, S. R., Ghosh, M. — 2009-06-26

We develop a novel empirical Bayesian framework for the semiparametric additive hazards regression model. The integrated likelihood, obtained by integration over the unknown prior of the nonparametric baseline cumulative hazard, can be maximized using standard statistical software. Unlike the corresponding full Bayes method, our empirical Bayes estimators of regression parameters, survival curves and their corresponding standard errors have easily computed closed-form expressions and require no elicitation of hyperparameters of the prior. The method guarantees a monotone estimator of the survival function and accommodates time-varying regression coefficients and covariates. To facilitate frequentist-type inference based on large-sample approximation, we present the asymptotic properties of the semiparametric empirical Bayes estimates. We illustrate the implementation and advantages of our methodology with a reanalysis of a survival dataset and a simulation study.

Induced smoothing for the semiparametric accelerated failure time model: asymptotics and extensions to clustered data

Johnson, L. M., Strawderman, R. L. — 2009-06-25

This paper extends the induced smoothing procedure of Brown & Wang (2006) for the semiparametric accelerated failure time model to the case of clustered failure time data. The resulting procedure permits fast and accurate computation of regression parameter estimates and standard errors using simple and widely available numerical methods, such as the Newton–Raphson algorithm. The regression parameter estimates are shown to be strongly consistent and asymptotically normal; in addition, we prove that the asymptotic distribution of the smoothed estimator coincides with that obtained without the use of smoothing. This establishes a key claim of Brown & Wang (2006) for the case of independent failure time data and also extends such results to the case of clustered data. Simulation results show that these smoothed estimates perform as well as those obtained using the best available methods at a fraction of the computational cost.

Pseudo-partial likelihood for proportional hazards models with biased-sampling data

Tsai, W. Y. — 2009-06-24

We obtain a pseudo-partial likelihood for proportional hazards models with biased-sampling data by embedding the biased-sampling data into left-truncated data. The log pseudo-partial likelihood of the biased-sampling data is the expectation of the log partial likelihood of the left-truncated data conditioned on the observed data. In addition, asymptotic properties of the estimator that maximize the pseudo-partial likelihood are derived. Applications to length-biased data, biased samples with right censoring and proportional hazards models with missing covariates are discussed.

Pseudo-partial likelihood estimators for the Cox regression model with missing covariates

Luo, X., Tsai, W. Y., Xu, Q. — 2009-06-22

By embedding the missing covariate data into a left-truncated and right-censored survival model, we propose a new class of weighted estimating functions for the Cox regression model with missing covariates. The resulting estimators, called the pseudo-partial likelihood estimators, are shown to be consistent and asymptotically normal. A simulation study demonstrates that, compared with the popular inverse-probability weighted estimators, the new estimators perform better when the observation probability is small and improve efficiency of estimating the missing covariate effects. Application to a practical example is reported.

Markov models for accumulating mutations

Beerenwinkel, N., Sullivant, S. — 2009-06-05

We introduce and analyze a waiting time model for the accumulation of genetic changes. The continuous-time conjunctive Bayesian network is defined by a partially ordered set of mutations and by the rate of fixation of each mutation. The partial order encodes constraints on the order in which mutations can fixate in the population, shedding light on the mutational pathways underlying the evolutionary process. We study a censored version of the model and derive equations for an em algorithm to perform maximum likelihood estimation of the model parameters. We also show how to select the maximum likelihood partially ordered set. The model is applied to genetic data from cancer cells and from drug resistant human immunodeficiency viruses, indicating implications for diagnosis and treatment.

Objective Bayesian model selection in Gaussian graphical models

Carvalho, C. M., Scott, J. G. — 2009-05-04

This paper presents a default model-selection procedure for Gaussian graphical models that involves two new developments. First, we develop a default version of the hyper-inverse Wishart prior for restricted covariance matrices, called the hyper-inverse Wishart g-prior, and show how it corresponds to the implied fractional prior for selecting a graph using fractional Bayes factors. Second, we apply a class of priors that automatically handles the problem of multiple hypothesis testing. We demonstrate our methods on a variety of simulated examples, concluding with a real example analyzing covariation in mutual-fund returns. These studies reveal that the combined use of a multiplicity-correction prior on graphs and fractional Bayes factors for computing marginal likelihoods yields better performance than existing Bayesian methods.