Bootstrapping Malmquist Indices for Danish Seiners in the North Sea and Skagerrak

In connection with assessing how an ongoing development in fisheries management may change fishing activity, evaluation of Total Factor Productivity (TFP) change over a period, including efficiency, scale and technology changes, is an important tool. The Malmquist index, based on distance functions evaluated with Data Envelopment Analysis (DEA), is often employed to estimate TFP changes. DEA is generally gaining attention for evaluating efficiency and capacity in fisheries. One main criticism of DEA is that it does not have any statistical foundation, i.e. that it is not possible to make inference about DEA scores or related parameters. The bootstrap method for estimating confidence intervals of deterministic parameters can however be applied to estimate confidence intervals for DEA scores. This method is applied in the present paper for assessing TFP changes between 1987 and 1999 for the fleet of Danish seiners operating in the North Sea and the Skagerrak.     

Asymptotic Bias in Parameter Estimation of AR-Processes Using Recursive Least Squares with Exponential Forgetting

The recursive least squares technique is often extended with exponential forgetting as a tool for parameter estimation in time-varying systems. The distribution of the resulting parameter estimates is, however, unknown when the forgetting factor is less than one. In this paper an approximative expression for bias of the recursively obtained parameter estimates in a time-invariant AR( n_a ) process with arbitrary noise is given, showing that the bias is non-zero and giving bounds on the approximation errors. Simulations confirm the approximation expressions.     

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.     

Nonparametric Bayes factors based on empirical likelihood ratios

Bayes methodology provides posterior distribution functions based on parametric likelihoods adjusted for prior distributions. A distribution-free alternative to the parametric likelihood is use of empirical likelihood (EL) techniques, well known in the context of nonparametric testing of statistical hypotheses. Empirical likelihoods have been shown to exhibit many of the properties of conventional parametric likelihoods. In this paper, we propose and examine Bayes factors (BF) methods that are derived via the EL ratio approach. Following Kass and Wasserman (1995), we consider Bayes factors type decision rules in the context of standard statistical testing techniques. We show that the asymptotic properties of the proposed procedure are similar to the classical BF's asymptotic operating characteristics. Although we focus on hypothesis testing, the proposed approach also yields confidence interval estimators of unknown parameters. Monte Carlo simulations were conducted to evaluate the theoretical results as well as to demonstrate the power of the proposed test.     

Partially Accelerated Life Tests for the Weibull Distribution Under Multiply Censored Data

This article aims to estimate the parameters of the Weibull distribution in step-stress partially accelerated life tests under multiply censored data. The step partially acceleration life test is that all test units are first run simultaneously under normal conditions for a pre-specified time, and the surviving units are then run under accelerated conditions until a predetermined censoring time. The maximum likelihood estimates are used to obtaining the parameters of the Weibull distribution and the acceleration factor under multiply censored data. Additionally, the confidence intervals for the estimators are obtained. Simulation results show that the maximum likelihood estimates perform well in most cases in terms of the mean bias, errors in the root mean square and the coverage rate. An example is used to illustrate the performance of the proposed approach.     

Case–control genome-wide joint association study using semiparametric empirical model and approximate Bayes factor

We propose a semiparametric approach for the analysis of case–control genome-wide association study. Parametric components are used to model both the conditional distribution of the case status given the covariates and the distribution of genotype counts, whereas the distribution of the covariates are modelled nonparametrically. This yields a direct and joint modelling of the case status, covariates and genotype counts, and gives a better understanding of the disease mechanism and results in more reliable conclusions. Side information, such as the disease prevalence, can be conveniently incorporated into the model by an empirical likelihood approach and leads to more efficient estimates and a powerful test in the detection of disease-associated SNPs. Profiling is used to eliminate a nuisance nonparametric component, and the resulting profile empirical likelihood estimates are shown to be consistent and asymptotically normal. For the hypothesis test on disease association, we apply the approximate Bayes factor (ABF) which is computationally simple and most desirable in genome-wide association studies where hundreds of thousands to a million genetic markers are tested. We treat the approximate Bayes factor as a hybrid Bayes factor which replaces the full data by the maximum likelihood estimates of the parameters of interest in the full model and derive it under a general setting. The deviation from Hardy–Weinberg Equilibrium (HWE) is also taken into account and the ABF for HWE using cases is shown to provide evidence of association between a disease and a genetic marker. Simulation studies and an application are further provided to illustrate the utility of the proposed methodology.     

Cointegration Detection Using Dynamic Factor Models

A method of information-criterion-based cointegration detection using dynamic factor models is proposed. The results of the data-based and non data-based Monte Carlo simulations suggest that this method is as effective as conventional hypothesis-testing methods. In the proposed method, an observed multivariate time series is described in terms of common stochastic trends plus stationary autoregressive cycles. Then the best model is selected from among alternative models obtained by changing the number of common stochastic trends, on the basis of information criteria. Consequently, the cointegration rank is determined on the basis of the selected model. Two advantages of the proposed method are also discussed.     

Computational algorithms for the factor model

Algorithms for computing the maximum likelihood estimators and the estimated covariance matrix of the estimators of the factor model are derived. The algorithms are particularly suitable for large matrices and for samples that give zero estimates of some error variances. A method of constructing estimators for reduced models is presented. The algorithms can also be used for the multivariate errors-in-variables model with known error covariance matrix.     

Practical bayesian approaches to the analystcs of a 2×2 contingency table with incompletely categorized data

To assess the efficacy of a treatment, patients are administered a pre-test, the treatment, and a post-test (identical to the pre-test). These patients are then categorized according to their outcomes observed on both tests,e.g., (S,S), (S,F), etc. Also, we observe "incomplete" information on the pre-tests' outcomes for some patients and the results of only the post-test being known for thers, A Bayesian framework is fit to the problem and Bayes factors, posterior odds ratios, and utility functions are given to evaluate th e treatment, A method of assessing the prior distribution is specified and a numerical example is worked.     

A comparison of random balance and two-stage group screening designs: A case study

In this paper we focus on the problem of supersaturated (fewer runs than factors) screening experiments. We consider two major types of designs which have been proposed in this situ¬ation: random balance and two-stage group screening. We discuss the relative merits and demerits of each strategy. In addition, we compare the performance of these strategies by means of a case study in which 100 factors are screened in 20,42,62, and 84 runs.