A comparison of models using removal effort to estimate animal abundance

This paper compares methods for modeling the probability of removal when variable amounts of removal effort are present. A hierarchical modeling framework can produce estimates of animal abundance and detection from replicated removal counts taken at different locations in a region of interest. A common method of specifying variation in detection probabilities across locations or replicates is with a logistic model that incorporates relevant detection covariates. As an alternative to this logistic model, we propose using a catch–effort (CE) model to account for heterogeneity in detection when a measure of removal effort is available for each removal count. This method models the probability of detection as a nonlinear function of removal effort and a removal probability parameter that can vary spatially. Simulation results demonstrate that the CE model can effectively estimate abundance and removal probabilities when average removal rates are large but both the CE and logistic models tend to produce biased estimates as average removal rates decrease. We also found that the CE model fits better than logistic models when estimating wild turkey abundance using harvest and hunter counts collected by the Minnesota Department of Natural Resources during the spring turkey hunting season.     

A NORMAL APPROXIMATION TO THE FISHER DISTRIBUTION

A simple normal approximation is given for the joint probability density function of the polar co-ordinates (θ, ψ) of a random vector following the Fisher distribution with arbitrary mean direction (θ₀, ψ₀). The approximation leads to simple inference procedures which are particularly useful in regression models. Conditions for the adequacy of the approximation are investigated and summarized in tabular form.     

Estimating functions in indirect inference

Summary.  There are models for which the evaluation of the likelihood is infeasible in practice. For these models the Metropolis–Hastings acceptance probability cannot be easily computed. This is the case, for instance, when only departure times from a G / G /1 queue are observed and inference on the arrival and service distributions are required. Indirect inference is a method to estimate a parameter θ in models whose likelihood function does not have an analytical closed form, but from which random samples can be drawn for fixed values of θ . First an auxiliary model is chosen whose parameter β can be directly estimated. Next, the parameters in the auxiliary model are estimated for the original data, leading to an estimate     . The parameter β is also estimated by using several sampled data sets, simulated from the original model for different values of the original parameter θ . Finally, the parameter θ which leads to the best match to     is chosen as the indirect inference estimate. We analyse which properties an auxiliary model should have to give satisfactory indirect inference. We look at the situation where the data are summarized in a vector statistic T , and the auxiliary model is chosen so that inference on β is drawn from T only. Under appropriate assumptions the asymptotic covariance matrix of the indirect estimators is proportional to the asymptotic covariance matrix of T and componentwise inversely proportional to the square of the derivative, with respect to θ , of the expected value of T . We discuss how these results can be used in selecting good estimating functions. We apply our findings to the queuing problem.     

Exact Short Confidence Intervals from Discrete Data

Suppose that X is a discrete random variable whose possible values are {0, 1, 2,⋯} and whose probability mass function belongs to a family indexed by the scalar parameter θ . This paper presents a new algorithm for finding a 1 − α confidence interval for θ based on X which possesses the following three properties: (i) the infimum over θ of the coverage probability is 1 − α ; (ii) the confidence interval cannot be shortened without violating the coverage requirement; (iii) the lower and upper endpoints of the confidence intervals are increasing functions of the observed value x . This algorithm is applied to the particular case that X has a negative binomial distribution.     

Phase I trial design for drug combinations with Bayesian model averaging

Various statistical models have been proposed for two‐dimensional dose finding in drug‐combination trials. However, it is often a dilemma to decide which model to use when conducting a particular drug‐combination trial. We make a comprehensive comparison of four dose‐finding methods, and for fairness, we apply the same dose‐finding algorithm under the four model structures. Through extensive simulation studies, we compare the operating characteristics of these methods in various practical scenarios. The results show that different models may lead to different design properties and that no single model performs uniformly better in all scenarios. As a result, we propose using Bayesian model averaging to overcome the arbitrariness of the model specification and enhance the robustness of the design. We assign a discrete probability mass to each model as the prior model probability and then estimate the toxicity probabilities of combined doses in the Bayesian model averaging framework. During the trial, we adaptively allocated each new cohort of patients to the most appropriate dose combination by comparing the posterior estimates of the toxicity probabilities with the prespecified toxicity target. The simulation results demonstrate that the Bayesian model averaging approach is robust under various scenarios. Copyright © 2015 John Wiley & Sons, Ltd.     

Testing for Imperfect Debugging in Software Reliability

This paper continues the study of the software reliability model of Fakhre-Zakeri & Slud (1995), an "exponential order statistic model" in the sense of Miller (1986) with general mixing distribution, imperfect debugging and large-sample asymptotics reflecting increase of the initial number of bugs with software size. The parameters of the model are θ (proportional to the initial number of bugs in the software), G (·, μ) (the mixing df, with finite dimensional unknown parameter μ, for the rates λ _i with which the bugs in the software cause observable system failures), and p (the probability with which a detected bug is instantaneously replaced with another bug instead of being removed). Maximum likelihood estimation theory for (θ, p , μ) is applied to construct a likelihood-based score test for large sample data of the hypothesis of "perfect debugging" ( p = 0) vs "imperfect" ( p > 0) within the models studied. There are important models (including the Jelinski–Moranda) under which the score statistics with 1/√ n normalization are asymptotically degenerate. These statistics, illustrated on a software reliability data of Musa (1980), can serve nevertheless as important diagnostics for inadequacy of simple models     

Semiparametric methods for response-selective and missing data problems in regression

Suppose that data are generated according to the model f ( y | x ; θ ) g ( x ), where y is a response and x are covariates. We derive and compare semiparametric likelihood and pseudolikelihood methods for estimating θ for situations in which units generated are not fully observed and in which it is impossible or undesirable to model the covariate distribution. The probability that a unit is fully observed may depend on y , and there may be a subset of covariates which is observed only for a subsample of individuals. Our key assumptions are that the probability that a unit has missing data depends only on which of a finite number of strata that ( y , x ) belongs to and that the stratum membership is observed for every unit. Applications include case–control studies in epidemiology, field reliability studies and broad classes of missing data and measurement error problems. Our results make fully efficient estimation of θ feasible, and they generalize and provide insight into a variety of methods that have been proposed for specific problems.     

On Minimum Distance Estimation Using Kolmogorov-Lévy Type Metrics

Let X ₁, . . ., X_n be independent identically distributed random variables with a common continuous (cumulative) distribution function (d.f.) F , and F^_n the empirical d.f. (e.d.f.) based on X ₁, . . ., X_n . Let G be a smooth d.f. and Gθ = G (·–θ) its translation through θ∈ R . Using a Kolmogorov-Lévy type metric ρ_α defined on the space of d.f.s. on R , the paper derives both null and non-null limiting distributions of √ n [ ρ_α ( F_n , Gθ_n ) – ρ_α ( F, G_θ )], √ n (θ _n –θ) and √ nρ_α ( Gθ , Gθ ), where θ _n and θ are the minimum ρ_α -distance parameters for F_n and F from G , respectively. These distributions are known explicitly in important particular cases; with some complementary Monte Carlo simulations, they help us clarify our understanding of estimation using minimum distance methods and supremum type metrics. We advocate use of the minimum distance method with supremum type metrics in cases of non-null models. The resulting functionals are Hadamard differentiable and efficient. For small scale parameters the minimum distance functionals are close to medians of the parent distributions. The optimal small scale models result in minimum distance estimators having asymptotic variances very competitive and comparable with best known robust estimators.     

Estimation in Semiparametric Marginal Shared Gamma Frailty Models

The semiparametric marginal shared frailty models in survival analysis have the non–parametric hazard functions multiplied by a random frailty in each cluster, and the survival times conditional on frailties are assumed to be independent. In addition, the marginal hazard functions have the same form as in the usual Cox proportional hazard models. In this paper, an approach based on maximum likelihood and expectation–maximization is applied to semiparametric marginal shared gamma frailty models, where the frailties are assumed to be gamma distributed with mean 1 and variance θ. The estimates of the fixed–effect parameters and their standard errors obtained using this approach are compared in terms of both bias and efficiency with those obtained using the extended marginal approach. Similarly, the standard errors of our frailty variance estimates are found to compare favourably with those obtained using other methods. The asymptotic distribution of the frailty variance estimates is shown to be a 50–50 mixture of a point mass at zero and a truncated normal random variable on the positive axis for θ₀ = 0. Simulations demonstrate that, for θ₀ < 0, it is approximately an x −(100 − x )%, 0 ≤ x ≤ 50, mixture between a point mass at zero and a truncated normal random variable on the positive axis for small samples and small values of θ₀; otherwise, it is approximately normal.     

Ordering of Sequentially Sampled Exponential Experiments

Let X ₁, X ₂, ... be a sequence of i.i.d. random variables, X _i∼ F _θ, θ∈Θ. Let N ₁ and N ₂ be two stopping rules. For a class of exponential families { F _θ: θ∈Θ} we show that the experiment Y ₁ = ( X ₁, ..., X _N1) carries more statistical information than Y ₂ = ( X ₁, ..., x _N2) only if N ₁ is stochastically larger then N ₂     

Model fitting and inference under latent equilibrium processes

This paper presents a methodology for model fitting and inference in the context of Bayesian models of the type f(Y | X,θ)f(X|θ)f(θ), where Y is the (set of) observed data, θ is a set of model parameters and X is an unobserved (latent) stationary stochastic process induced by the first order transition model f(X ^(t+1)|X ^(t),θ), where X ^(t) denotes the state of the process at time (or generation) t. The crucial feature of the above type of model is that, given θ, the transition model f(X ^(t+1)|X ^(t),θ) is known but the distribution of the stochastic process in equilibrium, that is f(X|θ), is, except in very special cases, intractable, hence unknown. A further point to note is that the data Y has been assumed to be observed when the underlying process is in equilibrium. In other words, the data is not collected dynamically over time. We refer to such specification as a latent equilibrium process (LEP) model. It is motivated by problems in population genetics (though other applications are discussed), where it is of interest to learn about parameters such as mutation and migration rates and population sizes, given a sample of allele frequencies at one or more loci. In such problems it is natural to assume that the distribution of the observed allele frequencies depends on the true (unobserved) population allele frequencies, whereas the distribution of the true allele frequencies is only indirectly specified through a transition model. As a hierarchical specification, it is natural to fit the LEP within a Bayesian framework. Fitting such models is usually done via Markov chain Monte Carlo (MCMC). However, we demonstrate that, in the case of LEP models, implementation of MCMC is far from straightforward. The main contribution of this paper is to provide a methodology to implement MCMC for LEP models. We demonstrate our approach in population genetics problems with both simulated and real data sets. The resultant model fitting is computationally intensive and thus, we also discuss parallel implementation of the procedure in special cases.     

Predicting Turning Points Through the Integration of Multiple Models

A new method for forming composite turning-point (or other qualitative) forecasts is proposed. Rather than forming composite forecasts by the standard Bayesian approach with weights proportional to each model's posterior odds, weights are assigned to the individual models in proportion to the probability of each model's having the correct turning-point prediction. These probabilities are generated by logit models estimated with data on the models' past turning-point forecasts. An empirical application to gross national product/gross domestic product forecasting of 18 Organization for Economic Cooperation and Development countries demonstrates the potential benefits of the procedure     

On the efficiency of affine minimax rules in estimating a bounded multivariate normal mean

Problems involving bounded parameter spaces, for example T-minimax and minimax esyimation of bounded parameters, have received much attention in recent years. The existing literature is rich. In this paper we consider T-minimax estimation of a multivariate bounded normal mean by affine rules, and discuss the loss of efficiency due to the use of such rules instead of optimal, unrestricted rules. We also investigate the behavior of 'probability restricted' affine rules, i.e., rules that have a guaranteed large probability of being in the bounded parameter space of the problem.     

Large-scale Bayesian spatial modelling of air pollution for policy support

The potential effects of air pollution are a major concern both in terms of the environment and in relation to human health. In order to support environmental policy, there is a need for accurate measurements of the concentrations of pollutants at high geographical resolution over large regions. However, within such regions, there are likely to be areas where the monitoring information will be sparse and so methods are required to accurately predict concentrations. Set within a Bayesian framework, models are developed which exploit the relationships between pollution and geographical covariate information, such as land use, climate and transport variables together with spatial structure. Candidate models are compared based on their ability to predict a set of validation sites. The chosen model is used to perform large-scale prediction of nitrogen dioxide at a 1×1 km resolution for the entire EU. The models allow probabilistic statements to be made with regard to the levels of air pollution that might be experienced in each area. When combined with population data, such information can be invaluable in informing policy by indicating areas for which improvements may be given priority.     

Bayesian Robustness Modelling of Location and Scale Parameters

Abstract. The modelling process in Bayesian Statistics constitutes the fundamental stage of the analysis, since depending on the chosen probability laws the inferences may vary considerably. This is particularly true when conflicts arise between two or more sources of information. For instance, inference in the presence of an outlier (which conflicts with the information provided by the other observations) can be highly dependent on the assumed sampling distribution. When heavy‐tailed (e.g. t) distributions are used, outliers may be rejected whereas this kind of robust inference is not available when we use light‐tailed (e.g. normal) distributions. A long literature has established sufficient conditions on location‐parameter models to resolve conflict in various ways. In this work, we consider a location–scale parameter structure, which is more complex than the single parameter cases because conflicts can arise between three sources of information, namely the likelihood, the prior distribution for the location parameter and the prior for the scale parameter. We establish sufficient conditions on the distributions in a location–scale model to resolve conflicts in different ways as a single observation tends to infinity. In addition, for each case, we explicitly give the limiting posterior distributions as the conflict becomes more extreme.     

A mixture of experts latent position cluster model for social network data

Social network data represent the interactions between a group of social actors. Interactions between colleagues and friendship networks are typical examples of such data.The latent space model for social network data locates each actor in a network in a latent (social) space and models the probability of an interaction between two actors as a function of their locations. The latent position cluster model extends the latent space model to deal with network data in which clusters of actors exist — actor locations are drawn from a finite mixture model, each component of which represents a cluster of actors.A mixture of experts model builds on the structure of a mixture model by taking account of both observations and associated covariates when modeling a heterogeneous population. Herein, a mixture of experts extension of the latent position cluster model is developed. The mixture of experts framework allows covariates to enter the latent position cluster model in a number of ways, yielding different model interpretations.Estimates of the model parameters are derived in a Bayesian framework using a Markov Chain Monte Carlo algorithm. The algorithm is generally computationally expensive — surrogate proposal distributions which shadow the target distributions are derived, reducing the computational burden.The methodology is demonstrated through an illustrative example detailing relationships between a group of lawyers in the USA.     

The table look-up rule

The table look-up rule problem can be described by the question: what is a good way for the table to represent the decision regions in the N-dimensional measurement space. This paper describes a quickly implementable table look-up rule based on Ashby’s representation of sets in his constraint analysis. A decision region for category c in the N-dimensional measurement space is considered to be the intersection of the inverse projections of the decision regions determined for category c by Bayes rules in smaller dimensional projection spaces. Error bounds for this composite decision rule are derived: any entry in the confusion matrix for the composite decision rule is bounded above by the minimum of that entry taken over all the confusion matrices of the Bayes decision rules in the smaller dimensional projection spaces.

On simulated Gaussian Data, probability of error with the table look-up rule is comparable to the optimum Bayes rule.     

IMPROVING UPON THE BEST INVARIANT ESTIMATOR IN MULTIVARIATE LOCATION PROBLEMS

We are concerned with estimators which improve upon the best invariant estimator, in estimating a location parameter θ. If the loss function is L(θ - a) with L convex, we give sufficient conditions for the inadmissibility of δ₀(X) = X. If the loss is a weighted sum of squared errors, we find various classes of estimators δ which are better than δ₀. In general, δ is the convolution of δ₁ (an estimator which improves upon δ₀ outside of a compact set) with a suitable probability density in R^p. The critical dimension of inadmissibility depends on the estimator δ₁ We also give several examples of estimators δ obtained in this way and state some open problems.     

The Role of Classification Trees and Expert Knowledge in Building Bayesian Networks: A Case Study in Medicine

In clinical research an early and prompt detection of the risk class of a new patient may really play a crucial role in determining the effectiveness of the treatment and, consequently, achieving a satisfying prognosis of the patient's chances. There exists a number of popular rule-based algorithms for classification, whose performances are very attractive whenever data of large number of patients are available. However, when datasets only include data of a few hundred patients, the most common approaches give unstable results and developing effective decision-support systems become scientifically challenging. Since rules can be derived from different models as well as expert knowledge resources, each of them having its advantages and weaknesses, this article suggests a “hybrid” approach to address the classification problem when the number of patients is too small to effectively use a single technique only. The hybrid strategy was applied to a case study and its predictive performance was compared with performances of each single approach: due to the seriousness of a misclassification of high-risk patients, special attention was paid on the specificity. The results show that the hybrid strategy outperforms each single strategy involved.     

Eliciting prior information to enhance the predictive performance of bayesian graphical models

Both knowledge-based systems and statistical models are typically concerned with making predictions about future observables. Here we focus on assessment of predictive performance and provide two techniques for improving the predictive performance of Bayesian graphical models. First, we present Bayesian model averaging, a technique for accounting for model uncertainty.

Second, we describe a technique for eliciting a prior distribution for competing models from domain experts. We explore the predictive performance of both techniques in the context of a urological diagnostic problem.