Modelling udder infection data using copula models for quadruples

We study copula models for correlated infection times in the four udder quarters of dairy cows. Both a semi-parametric and a nonparametric approach are considered to estimate the marginal survival functions, taking into account the effect of a binary udder quarter level covariate. We use a two-stage estimation approach and we briefly discuss the asymptotic behaviour of the estimators obtained in the first and the second stage of the estimation. A pseudo-likelihood ratio test is used to select an appropriate copula from the power variance copula family that describes the association between the outcomes in a cluster. We propose a new bootstrap algorithm to obtain the p-value for this test. This bootstrap algorithm also provides estimates for the standard errors of the estimated parameters in the copula. The proposed methods are applied to the udder infection data. A small simulation study for a setting similar to the setting of the udder infection data gives evidence that the proposed method provides a valid approach to select an appropriate copula within the power variance copula family.     

Bayesian partial likelihood approach for tied observations

The Bayesian analysis based on the partial likelihood for Cox's proportional hazards model is frequently used because of its simplicity. The Bayesian partial likelihood approach is often justified by showing that it approximates the full Bayesian posterior of the regression coefficients with a diffuse prior on the baseline hazard function. This, however, may not be appropriate when ties exist among uncensored observations. In that case, the full Bayesian and Bayesian partial likelihood posteriors can be much different. In this paper, we propose a new Bayesian partial likelihood approach for many tied observations and justify its use.     

A comparison of nonparametric priors in hierarchical mixture modelling for AFT regression

We will pursue a Bayesian nonparametric approach in the hierarchical mixture modelling of lifetime data in two situations: density estimation, when the distribution is a mixture of parametric densities with a nonparametric mixing measure, and accelerated failure time (AFT) regression modelling, when the same type of mixture is used for the distribution of the error term. The Dirichlet process is a popular choice for the mixing measure, yielding a Dirichlet process mixture model for the error; as an alternative, we also allow the mixing measure to be equal to a normalized inverse-Gaussian prior, built from normalized inverse-Gaussian finite dimensional distributions, as recently proposed in the literature. Markov chain Monte Carlo techniques will be used to estimate the predictive distribution of the survival time, along with the posterior distribution of the regression parameters. A comparison between the two models will be carried out on the grounds of their predictive power and their ability to identify the number of components in a given mixture density.     

Copula-based regression models: A survey

In this review paper we collect several results about copula-based models, especially concerning regression models, by focusing on some insurance applications.     

R×C ecological inference: bounds, correlations, flexibility and transparency of assumptions

Summary.  Despite its potential pitfalls, ecological inference is an unavoidable part of some quantitative settings, including US voting rights litigation. In such applications, the analyst will typically encounter two-way tables with more than two rows and columns. Although several ecological inference methods are currently available for 2×2 tables, there are fewer options for analysing general R × C tables, and virtually none that model counts as opposed to fractions. We propose a count R × C method that respects the bounds deterministically, that allows for complex relationships between internal cell quantities, that is easily extensible and that results from transparent assumptions. We study the method via simulation, and then apply it to an example that is drawn from the state of Texas relevant to recent redistricting litigation there.     

Using Bayesian graphical models to model biases in observational studies and to combine multiple sources of data: application to low birth weight and water disinfection by-products

Summary.  Data in the social, behavioural and health sciences frequently come from observational studies instead of controlled experiments. In addition to random errors, observational data typically contain additional sources of uncertainty such as missing values, unmeasured confounders and selection biases. Also, the research question is often different from that which a particular source of data was designed to answer, and so not all relevant variables are measured. As a result, multiple sources of data are often necessary to identify the biases and to inform about different aspects of the research question. Bayesian graphical models provide a coherent way to connect a series of local submodels, based on different data sets, into a global unified analysis. We present a unified modelling framework that will account for multiple biases simultaneously and give more accurate parameter estimates than standard approaches. We illustrate our approach by analysing data from a study of water disinfection by-products and adverse birth outcomes in the UK.     

Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations

Summary.  Structured additive regression models are perhaps the most commonly used class of models in statistical applications. It includes, among others, (generalized) linear models, (generalized) additive models, smoothing spline models, state space models, semiparametric regression, spatial and spatiotemporal models, log-Gaussian Cox processes and geostatistical and geoadditive models. We consider approximate Bayesian inference in a popular subset of structured additive regression models, latent Gaussian models , where the latent field is Gaussian, controlled by a few hyperparameters and with non-Gaussian response variables. The posterior marginals are not available in closed form owing to the non-Gaussian response variables. For such models, Markov chain Monte Carlo methods can be implemented, but they are not without problems, in terms of both convergence and computational time. In some practical applications, the extent of these problems is such that Markov chain Monte Carlo sampling is simply not an appropriate tool for routine analysis. We show that, by using an integrated nested Laplace approximation and its simplified version, we can directly compute very accurate approximations to the posterior marginals. The main benefit of these approximations is computational: where Markov chain Monte Carlo algorithms need hours or days to run, our approximations provide more precise estimates in seconds or minutes. Another advantage with our approach is its generality, which makes it possible to perform Bayesian analysis in an automatic, streamlined way, and to compute model comparison criteria and various predictive measures so that models can be compared and the model under study can be challenged.     

Copula structure analysis

Summary.  We extend the standard approach of correlation structure analysis for dimension reduction of high dimensional statistical data. The classical assumption of a linear model for the distribution of a random vector is replaced by the weaker assumption of a model for the copula. For elliptical copulas a correlation-like structure remains, but different margins and non-existence of moments are possible. After introducing the new concept and deriving some theoretical results we observe in a simulation study the performance of the estimators: the theoretical asymptotic behaviour of the statistics can be observed even for small sample sizes. Finally, we show our method at work for a financial data set and explain differences between our copula-based approach and the classical approach. Our new method yielear models also.     

SEMIPARAMETRIC REGRESSION AND GRAPHICAL MODELS

Semiparametric regression models that use spline basis functions with penalization have graphical model representations. This link is more powerful than previously established mixed model representations of semiparametric regression, as a larger class of models can be accommodated. Complications such as missingness and measurement error are more naturally handled within the graphical model architecture. Directed acyclic graphs, also known as Bayesian networks, play a prominent role. Graphical model-based Bayesian 'inference engines', such as bugs and vibes , facilitate fitting and inference. Underlying these are Markov chain Monte Carlo schemes and recent developments in variational approximation theory and methodology.     

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.