Vector random fields with compactly supported covariance matrix functions

The objective of this paper is to construct covariance matrix functions whose entries are compactly supported, and to use them as building blocks to formulate other covariance matrix functions for second-order vector stochastic processes or random fields. In terms of the scale mixture of compactly supported covariance matrix functions, we derive a class of second-order vector stochastic processes on the real line whose direct and cross covariance functions are of Pólya type. Then some second-order vector random fields in R^d${\mathbb{R}}^d$ whose direct and cross covariance functions are compactly supported are constructed by using a convolution approach and a mixture approach.     

Model-based confidence bands for survival functions

This paper focuses on a novel method of developing one-sample confidence bands for survival functions from right censored data. The approach is model-based, relying on a parametric model for the conditional expectation of the censoring indicator given the observed minimum, and derives its strength from easy access to a good-fitting model among a plethora of choices available for binary response data. The substantive methodological contribution is in exploiting a semiparametric estimator of the survival function to produce improved simultaneous confidence bands. To obtain critical values for computing the confidence bands, a two-stage bootstrap approach that combines the classical bootstrap with the more recent model-based regeneration of censoring indicators is proposed and a justification of its asymptotic validity is also provided. Several different confidence bands are studied using the proposed approach. Numerical studies, including robustness of the proposed bands to misspecification, are carried out to check efficacy. The method is illustrated using two lung cancer data sets.     

Random-effect models with singular precision

We show that smoothing spline, intrinsic autoregression (IAR) and state-space model can be formulated as partially specified random-effect model with singular precision (SP). Various fitting methods have been suggested for the aforementioned models and this paper investigates the relationships among them, once the models have been placed under a single framework. Some methods have been previously shown to give the best linear unbiased predictors (BLUPs) under some random-effect models and here we show that they are in fact uniformly BLUPs (UBLUPs) under a class of models that are generated by the SP of random effects. We offer some new interpretations of the UBLUPs under models of SP and define BLUE and BLUP in these partially specified models without having to specify the covariance. We also show how the full likelihood inferences for random-effect models can be made for these models, so that the maximum likelihood (ML) and restricted maximum likelihood (REML) estimators can be used for the smoothing parameters in splines, etc.     

Lower posterior death probabilities from a quick medical response in road traffic accidents

Introduction: We use data from Spain on roads and motorways traffic accidents in May 2004 to quantify the statistical association between quick medical response time and mortality rate. Method: Probit and logit parameters are estimated by a Bayesian method in which samples from the posterior densities are obtained through an MCMC simulation scheme. We provide posterior credible intervals and posterior partial effects of a quick medical response at several time levels over which we express our prior beliefs. Results: A reduction of 5 min, from a 25-min response-time level, is associated with lower posterior probabilities of death in roads and motorways accidents of 24% and 30%, respectively.     

Parameter estimation of nonlinear mixed-effects models using first-order conditional linearization and the EM algorithm

Nonlinear mixed-effects (NLME) models are flexible enough to handle repeated-measures data from various disciplines. In this article, we propose both maximum-likelihood and restricted maximum-likelihood estimations of NLME models using first-order conditional expansion (FOCE) and the expectation–maximization (EM) algorithm. The FOCE-EM algorithm implemented in the ForStat procedure SNLME is compared with the Lindstrom and Bates (LB) algorithm implemented in both the SAS macro NLINMIX and the S-Plus/R function nlme in terms of computational efficiency and statistical properties. Two realworld data sets an orange tree data set and a Chinese fir (Cunninghamia lanceolata) data set, and a simulated data set were used for evaluation. FOCE-EM converged for all mixed models derived from the base model in the two realworld cases, while LB did not, especially for the models in which random effects are simultaneously considered in several parameters to account for between-subject variation. However, both algorithms had identical estimated parameters and fit statistics for the converged models. We therefore recommend using FOCE-EM in NLME models, particularly when convergence is a concern in model selection.     

Bayesian model comparison for compartmental models with applications in positron emission tomography

We develop strategies for Bayesian modelling as well as model comparison, averaging and selection for compartmental models with particular emphasis on those that occur in the analysis of positron emission tomography (PET) data. Both modelling and computational issues are considered. Biophysically inspired informative priors are developed for the problem at hand, and by comparison with default vague priors it is shown that the proposed modelling is not overly sensitive to prior specification. It is also shown that an additive normal error structure does not describe measured PET data well, despite being very widely used, and that within a simple Bayesian framework simultaneous parameter estimation and model comparison can be performed with a more general noise model. The proposed approach is compared with standard techniques using both simulated and real data. In addition to good, robust estimation performance, the proposed technique provides, automatically, a characterisation of the uncertainty in the resulting estimates which can be considerable in applications such as PET.     

Bayesian factor models in characterizing molecular adaptation

Assessing the selective influence of amino acid properties is important in understanding evolution at the molecular level. A collection of methods and models has been developed in recent years to determine if amino acid sites in a given DNA sequence alignment display substitutions that are altering or conserving a prespecified set of amino acid properties. Residues showing an elevated number of substitutions that favorably alter a physicochemical property are considered targets of positive natural selection. Such approaches usually perform independent analyses for each amino acid property under consideration, without taking into account the fact that some of the properties may be highly correlated. We propose a Bayesian hierarchical regression model with latent factor structure that allows us to determine which sites display substitutions that conserve or radically change a set of amino acid properties, while accounting for the correlation structure that may be present across such properties. We illustrate our approach by analyzing simulated data sets and an alignment of lysin sperm DNA.     

Block and Basu bivariate lifetime distribution in the presence of cure fraction

This paper presents estimates for the parameters included in the Block and Basu bivariate lifetime distributions in the presence of covariates and cure fraction, applied to analyze survival data when some individuals may never experience the event of interest and two lifetimes are associated with each unit. A Bayesian procedure is used to get point and confidence intervals for the unknown parameters. Posterior summaries of interest are obtained using standard Markov Chain Monte Carlo methods in rjags package for R software. An illustration of the proposed methodology is given for a Diabetic Retinopathy Study data set.     

A longitudinal analysis of infant and senescent mortality using mixture models

We construct a mixture distribution including infant, exogenous and Gompertzian/non-Gompertzian senescent mortality. Using mortality data from Swedish females 1751–, we show that this outperforms models without these features, and compare its trends in cohort and period mortality over time. We find an almost complete disappearance of exogenous mortality within the last century of period mortality, with cohort mortality approaching the same limits. Both Gompertzian and non-Gompertzian senescent mortality are consistently present, with the estimated balance between them oscillating constantly. While the parameters of the latter appear to be trending over time, the parameters of the former do not.