A BAYESIAN HIERARCHICAL MODEL FOR POISSON RATE AND REPORTING-PROBABILITY INFERENCE USING DOUBLE SAMPLING

We analyse a combination of errant count data subject to under‐reported counts and inerrant count data to estimate multiple Poisson rates and reporting probabilities of cervical cancer for four European countries. Our analysis uses a Bayesian hierarchical model. Using a simulation study, we demonstrate the efficacy of our new simultaneous inference method and compare the utility of our method with an empirical Bayes approach developed by Fader and Hardie (J. Appl. Statist., 2000).     

ESTIMATION, PREDICTION AND INFERENCE FOR THE LASSO RANDOM EFFECTS MODEL

The least absolute shrinkage and selection operator (LASSO) can be formulated as a random effects model with an associated variance parameter that can be estimated with other components of variance. In this paper, estimation of the variance parameters is performed by means of an approximation to the marginal likelihood of the observed outcomes. The approximation is based on an alternative but equivalent formulation of the LASSO random effects model. Predictions can be made using point summaries of the predictive distribution of the random effects given the data with the parameters set to their estimated values. The standard LASSO method uses the mode of this distribution as the predictor. It is not the only choice, and a number of other possibilities are defined and empirically assessed in this article. The predictive mode is competitive with the predictive mean (best predictor), but no single predictor performs best across in all situations. Inference for the LASSO random effects is performed using predictive probability statements, which are more appropriate under the random effects formulation than tests of hypothesis.     

NON‐PARAMETRIC BAYESIAN INFERENCE FOR INHOMOGENEOUS MARKOV POINT PROCESSES

With reference to a specific dataset, we consider how to perform a flexible non‐parametric Bayesian analysis of an inhomogeneous point pattern modelled by a Markov point process, with a location‐dependent first‐order term and pairwise interaction only. A priori we assume that the first‐order term is a shot noise process, and that the interaction function for a pair of points depends only on the distance between the two points and is a piecewise linear function modelled by a marked Poisson process. Simulation of the resulting posterior distribution using a Metropolis–Hastings algorithm in the ‘conventional’ way involves evaluating ratios of unknown normalizing constants. We avoid this problem by applying a recently introduced auxiliary variable technique. In the present setting, the auxiliary variable used is an example of a partially ordered Markov point process model.     

BAYESIAN SUBSET SELECTION AND MODEL AVERAGING USING A CENTRED AND DISPERSED PRIOR FOR THE ERROR VARIANCE

This article proposes a new data‐based prior distribution for the error variance in a Gaussian linear regression model, when the model is used for Bayesian variable selection and model averaging. For a given subset of variables in the model, this prior has a mode that is an unbiased estimator of the error variance but is suitably dispersed to make it uninformative relative to the marginal likelihood. The advantage of this empirical Bayes prior for the error variance is that it is centred and dispersed sensibly and avoids the arbitrary specification of hyperparameters. The performance of the new prior is compared to that of a prior proposed previously in the literature using several simulated examples and two loss functions. For each example our paper also reports results for the model that orthogonalizes the predictor variables before performing subset selection. A real example is also investigated. The empirical results suggest that for both the simulated and real data, the performance of the estimators based on the prior proposed in our article compares favourably with that of a prior used previously in the literature.     

A BAYESIAN SIMULATION APPROACH TO INFERENCE ON A MULTI‐STATE LATENT FACTOR INTENSITY MODEL

The influence of economic conditions on the movement of a variable between states (for example a change in credit rating from A to B) can be modelled using a multi‐state latent factor intensity framework. Estimation of this type of model is, however, not straightforward, as transition probabilities are involved and the model contains a few highly analytically intractable distributions. In this paper, a Bayesian approach is adopted to manage the distributions. The innovation in the sampling algorithm used to obtain the posterior distributions of the model parameters includes a particle filter step and a Metropolis–Hastings step within a Gibbs sampler. The feasibility and accuracy of the proposed sampling algorithm is supported with a few simulated examples. The paper contains an application concerning what caused 1049 firms to change their credit ratings over a span of ten years.     

BAYESIAN ANALYSIS OF THE ADDITIVE MIXED MODEL FOR RANDOMIZED BLOCK DESIGNS

This paper deals with the Bayesian analysis of the additive mixed model experiments. Consider b randomly chosen subjects who respond once to each of t treatments. The subjects are treated as random effects and the treatment effects are fixed. Suppose that some prior information is available, thus motivating a Bayesian analysis. The Bayesian computation, however, can be difficult in this situation, especially when a large number of treatments is involved. Three computational methods are suggested to perform the analysis. The exact posterior density of any parameter of interest can be simulated based on random realizations taken from a restricted multivariate t distribution. The density can also be simulated using Markov chain Monte Carlo methods. The simulated density is accurate when a large number of random realizations is taken. However, it may take substantial amount of computer time when many treatments are involved. An alternative Laplacian approximation is discussed. The Laplacian method produces smooth and very accurate approximates to posterior densities, and takes only seconds of computer time. An example of a pipeline cracks experiment is used to illustrate the Bayesian approaches and the computational methods.     

A MODIFIED GROWTH CURVE MODEL AND ITS APPLICATION TO CLINICAL STUDIES

This paper considers a technique for applying growth curve analysis to data which are correlated across different groups. The method is illustrated using a study comparing three methods of suctioning an endotracheal tube.     

RANDOMIZED SEARCH STRATEGIES FOR FINDING OPTIMAL OR NEAR OPTIMAL BLOCK AND ROW-COLUMN DESIGNS

We consider a family of effective and efficient strategies for generating experimental designs of several types with high efficiency. These strategies employ randomized search directions and at some stages allow the possibility of taking steps in a direction of decreasing efficiency in an effort to avoid local optima. Hence our strategies have some affinity with the simulated annealing algorithm of combinatorial optimization. The methods work well and compare favourably with other search strategies. We have implemented them for incomplete block designs, optionally resolvable, and for row-column designs.     

CONDITIONAL INFERENCE PROCEDURES FOR THE PARETO AND POWER FUNCTION DISTRIBUTIONS BASED ON TYPE-II RIGHT CENSORED SAMPLES

In this paper we consider conditional inference procedures for the Pareto and power function distributions. We develop procedures for obtaining confidence intervals for the location and scale parameters as well as upper and lower n probability tolerance intervals for a proportion g, given a Type-II right censored sample from the corresponding distribution. The intervals are exact, and are obtained by conditioning on the observed values of the ancillary statistics. Since, for each distribution, the procedures assume that a shape parameter x is known, a sensitivity analysis is also carried out to see how the procedures are affected by changes in x.     

ESTIMATING BAYESIAN NETWORKS FOR HIGH‐DIMENSIONAL DATA WITH COMPLEX MEAN STRUCTURE AND RANDOM EFFECTS

The estimation of Bayesian networks given high‐dimensional data, in particular gene expression data, has been the focus of much recent research. Whilst there are several methods available for the estimation of such networks, these typically assume that the data consist of independent and identically distributed samples. It is often the case, however, that the available data have a more complex mean structure, plus additional components of variance, which must then be accounted for in the estimation of a Bayesian network. In this paper, score metrics that take account of such complexities are proposed for use in conjunction with score‐based methods for the estimation of Bayesian networks. We propose first, a fully Bayesian score metric, and second, a metric inspired by the notion of restricted maximum likelihood. We demonstrate the performance of these new metrics for the estimation of Bayesian networks using simulated data with known complex mean structures. We then present the analysis of expression levels of grape‐berry genes adjusting for exogenous variables believed to affect the expression levels of the genes. Demonstrable biological effects can be inferred from the estimated conditional independence relationships and correlations amongst the grape‐berry genes.     

OPTIMALITY OF NONPARAMETRIC TESTS FOR ASSOCIATION BETWEEN SURVIVAL TIME AND CONTINUOUS COVARIATES

Abstract

Recently, Chen (Chen, Z. (2000 Chen, Z. 2000. A new two-parameter lifetime distribution with bathtub-shape or increasing failure rate function. Statistics &; Probability Letters, 49: 155–161. [Crossref], [Web of Science ®] , [Google Scholar]). A new two-parameter lifetime distribution with bathtub-shape or increasing failure rate function. Statistics &; Probability Letters 49:155–161.) proposed a two-parameter model that can be used to model bathtub-shaped failure rate. Although this model has several interesting properties, it does not contain a scale parameter and hence not flexible in modeling real data. A generalized model including the scale parameter has shown to be interesting and it has the traditional Weibull distribution as an asymptotic case. In this article, a detailed analysis of this model is presented. Shapes of the density and failure rate function are studied. The asymptotic confidence intervals for the parameters are also derived from the Fisher information matrix. The likelihood ratio test is applied to test the goodness of fit of Weibull extension model. Some examples are shown to illustrate the application of the model and analysis.     

A MULTIVARIATE NORMAL MODEL FOR PEDIGREE AND LONGITUDINAL DATA AND THE SOFTWARE 'FISHER'

In 1918 R.A. Fisher published an interpretation of covariation between relatives in terms of Mendelian inheritance, which has allowed inference on genetic and environmental components of variation from plant, animal and human pedigree data. Fisher had introduced maximum likelihood six years earlier. His 1918 paper abo contained the basics of linear regression and decomposition of variance. These concepts have now been united to allow flexible modelling of the mean and covariance structure of non-independent data on continuous traits, using maximum likelihood under a multivariate normal assumption. FISHER is a software package, designed for pedigree analysis and easily adapted for repeated measures and longitudinal data analysis. A range of applications illustrate FISHER as a useful statistical tool. Issues related to assumptions, tests-of-fit, and robustness of inference are discussed.     

CAUSAL GRAPHICAL MODELS IN SYSTEMS GENETICS: A UNIFIED FRAMEWORK FOR JOINT INFERENCE OF CAUSAL NETWORK AND GENETIC ARCHITECTURE FOR CORRELATED PHENOTYPES

Causal inference approaches in systems genetics exploit quantitative trait loci (QTL) genotypes to infer causal relationships among phenotypes. The genetic architecture of each phenotype may be complex, and poorly estimated genetic architectures may compromise the inference of causal relationships among phenotypes. Existing methods assume QTLs are known or inferred without regard to the phenotype network structure. In this paper we develop a QTL-driven phenotype network method (QTLnet) to jointly infer a causal phenotype network and associated genetic architecture for sets of correlated phenotypes. Randomization of alleles during meiosis and the unidirectional influence of genotype on phenotype allow the inference of QTLs causal to phenotypes. Causal relationships among phenotypes can be inferred using these QTL nodes, enabling us to distinguish among phenotype networks that would otherwise be distribution equivalent. We jointly model phenotypes and QTLs using homogeneous conditional Gaussian regression models, and we derive a graphical criterion for distribution equivalence. We validate the QTLnet approach in a simulation study. Finally, we illustrate with simulated data and a real example how QTLnet can be used to infer both direct and indirect effects of QTLs and phenotypes that co-map to a genomic region.     

ASSOCIATIONS BETWEEN AIR POLLUTION AND HOSPITAL VISITS FOR CARDIOVASCULAR DISEASES IN THE ELDERLY IN SYDNEY USING BAYESIAN STATISTICAL METHODS

Using generalized linear models (GLMs), Jalaludin  et al. (2006;  J. Exposure Analysis and Epidemiology   16 , 225–237) studied the association between the daily number of visits to emergency departments for cardiovascular disease by the elderly (65+) and five measures of ambient air pollution. Bayesian methods provide an alternative approach to classical time series modelling and are starting to be more widely used. This paper considers Bayesian methods using the dataset used by Jalaludin  et al.  (2006) , and compares the results from Bayesian methods with those obtained by Jalaludin  et al.  (2006) using GLM methods.     

A STATISTICAL MODEL FOR DUPLICATE TOURNAMENTS IN GAMES OF LUCK AND SKILL

Many games played between two contestants start with a random deal, which introduces luck from the deal. The concept of ‘duplication’, commonly employed in Bridge tournaments, can be used to nullify that luck in a tournament. This paper poses a model for the contest between any two players and analyses the model for a tournament which employs the duplication principle. Two example tournaments on a new game are analysed.     

DECOMPOSITIONS FOR CONDITIONAL SYMMETRY MODEL INTO PALINDROMIC SYMMETRY AND MODIFIED MARGINAL HOMOGENEITY MODELS

For square contingency tables with ordered categories, the conditional symmetry model is decomposed into the palindromic symmetry and the modified marginal homogeneity models, and moreover into the generalized palindromic symmetry model and two other models. The data on unaided vision first analysed by Stuart (1953, 1955) is analysed again by using the decompositions.     

ESTIMATION OF GUARANTEE TIME AND MEAN LIFE AFTER WARRANTY FOR TWO-PARAMETER EXPONENTIAL FAILURE MODEL

Suppose manufactured items have failure times distributed with the two-parameter exponential density function à-^le-(x-μ)/à (x≥μ≥0). The paper considers estimation of the guarantee time μ and mean life after warranty à. Properties of various estimators are given for both separate and simultaneous estimation of μ and à. Criteria for comparing estimators are entropy loss, LINEX loss, and (generalized) Pitman nearness.     

A BRANCHING PROCESS MODEL FOR FLOW CYTOMETRY AND BUDDING INDEX MEASUREMENTS IN CELL SYNCHRONY EXPERIMENTS

We present a flexible branching process model for cell population dynamics in synchrony/time-series experiments used to study important cellular processes. Its formulation is constructive, based on an accounting of the unique cohorts in the population as they arise and evolve over time, allowing it to be written in closed form. The model can attribute effects to subsets of the population, providing flexibility not available using the models historically applied to these populations. It provides a tool for in silico synchronization of the population and can be used to deconvolve population-level experimental measurements, such as temporal expression profiles. It also allows for the direct comparison of assay measurements made from multiple experiments. The model can be fit either to budding index or DNA content measurements, or both, and is easily adaptable to new forms of data. The ability to use DNA content data makes the model applicable to almost any organism. We describe the model and illustrate its utility and flexibility in a study of cell cycle progression in the yeast Saccharomyces cerevisiae.