A robust QTL mapping procedure

In quantitative trait linkage studies using experimental crosses, the conventional normal location-shift model or other parameterizations may be unnecessarily restrictive. We generalize the mapping problem to a genuine nonparametric setup and provide a robust estimation procedure for the situation where the underlying phenotype distributions are completely unspecified. Classical Wilcoxon–Mann–Whitney statistics are employed for point and interval estimation of QTL positions and effects.     

Order statistics from trivariate normal and -distributions in terms of generalized skew-normal and skew- distributions

We consider here a generalization of the skew-normal distribution, GSN(λ₁,λ₂,ρ), defined through a standard bivariate normal distribution with correlation ρ, which is a special case of the unified multivariate skew-normal distribution studied recently by Arellano-Valle and Azzalini [2006. On the unification of families of skew-normal distributions. Scand. J. Statist. 33, 561–574]. We then present some simple and useful properties of this distribution and also derive its moment generating function in an explicit form. Next, we show that distributions of order statistics from the trivariate normal distribution are mixtures of these generalized skew-normal distributions; thence, using the established properties of the generalized skew-normal distribution, we derive the moment generating functions of order statistics, and also present expressions for means and variances of these order statistics.Next, we introduce a generalized skew-t_ν distribution, which is a special case of the unified multivariate skew-elliptical distribution presented by Arellano-Valle and Azzalini [2006. On the unification of families of skew-normal distributions. Scand. J. Statist. 33, 561–574] and is in fact a three-parameter generalization of Azzalini and Capitanio's [2003. Distributions generated by perturbation of symmetry with emphasis on a multivariate skew t distribution. J. Roy. Statist. Soc. Ser. B 65, 367–389] univariate skew-t_ν form. We then use the relationship between the generalized skew-normal and skew-t_ν distributions to discuss some properties of generalized skew-t_ν as well as distributions of order statistics from bivariate and trivariate t_ν distributions. We show that these distributions of order statistics are indeed mixtures of generalized skew-t_ν distributions, and then use this property to derive explicit expressions for means and variances of these order statistics.     

Hypotheses testing: Poisson versus stress-release

We consider the problem of hypotheses testing with the basic simple hypothesis: observed sequence of points corresponds to stationary Poisson process with known intensity against a composite one-sided parametric alternative that this is a stress-release point process. The underlying family of measures is locally asymptotically quadratic and we describe the behavior of score-function, likelihood ratio and Wald tests in the asymptotics of large samples. The results of numerical simulations are presented.     

Nonparametric density deconvolution by weighted kernel estimators

Nonparametric density estimation in the presence of measurement error is considered. The usual kernel deconvolution estimator seeks to account for the contamination in the data by employing a modified kernel. In this paper a new approach based on a weighted kernel density estimator is proposed. Theoretical motivation is provided by the existence of a weight vector that perfectly counteracts the bias in density estimation without generating an excessive increase in variance. In practice a data driven method of weight selection is required. Our strategy is to minimize the discrepancy between a standard kernel estimate from the contaminated data on the one hand, and the convolution of the weighted deconvolution estimate with the measurement error density on the other hand. We consider a direct implementation of this approach, in which the weights are optimized subject to sum and non-negativity constraints, and a regularized version in which the objective function includes a ridge-type penalty. Numerical tests suggest that the weighted kernel estimation can lead to tangible improvements in performance over the usual kernel deconvolution estimator. Furthermore, weighted kernel estimates are free from the problem of negative estimation in the tails that can occur when using modified kernels. The weighted kernel approach generalizes to the case of multivariate deconvolution density estimation in a very straightforward manner.     

Using relative utility curves to evaluate risk prediction

Summary.  Because many medical decisions are based on risk prediction models that are constructed from medical history and results of tests, the evaluation of these prediction models is important. This paper makes five contributions to this evaluation: the relative utility curve which gauges the potential for better prediction in terms of utilities, without the need for a reference level for one utility, while providing a sensitivity analysis for misspecification of utilities, the relevant region, which is the set of values of prediction performance that are consistent with the recommended treatment status in the absence of prediction, the test threshold, which is the minimum number of tests that would be traded for a true positive prediction in order for the expected utility to be non-negative, the evaluation of two-stage predictions that reduce test costs and connections between various measures of performance of prediction. An application involving the risk of cardiovascular disease is discussed.     

A re-evaluation of random-effects meta-analysis

Summary.  Meta-analysis in the presence of unexplained heterogeneity is frequently undertaken by using a random-effects model, in which the effects underlying different studies are assumed to be drawn from a normal distribution. Here we discuss the justification and interpretation of such models, by addressing in turn the aims of estimation, prediction and hypothesis testing. A particular issue that we consider is the distinction between inference on the mean of the random-effects distribution and inference on the whole distribution. We suggest that random-effects meta-analyses as currently conducted often fail to provide the key results, and we investigate the extent to which distribution-free, classical and Bayesian approaches can provide satisfactory methods. We conclude that the Bayesian approach has the advantage of naturally allowing for full uncertainty, especially for prediction. However, it is not without problems, including computational intensity and sensitivity to a priori judgements. We propose a simple prediction interval for classical meta-analysis and offer extensions to standard practice of Bayesian meta-analysis, making use of an example of studies of 'set shifting' ability in people with eating disorders.     

Automating and evaluating reversible jump MCMC proposal distributions

The reversible jump Markov chain Monte Carlo (MCMC) sampler (Green in Biometrika 82:711–732, 1995) has become an invaluable device for Bayesian practitioners. However, the primary difficulty with the sampler lies with the efficient construction of transitions between competing models of possibly differing dimensionality and interpretation. We propose the use of a marginal density estimator to construct between-model proposal distributions. This provides both a step towards black-box simulation for reversible jump samplers, and a tool to examine the utility of common between-model mapping strategies. We compare the performance of our approach to well established alternatives in both time series and mixture model examples.     

Transformed generalized linear models

The estimation of data transformation is very useful to yield response variables satisfying closely a normal linear model. Generalized linear models enable the fitting of models to a wide range of data types. These models are based on exponential dispersion models. We propose a new class of transformed generalized linear models to extend the Box and Cox models and the generalized linear models. We use the generalized linear model framework to fit these models and discuss maximum likelihood estimation and inference. We give a simple formula to estimate the parameter that index the transformation of the response variable for a subclass of models. We also give a simple formula to estimate the r$r$th moment of the original dependent variable. We explore the possibility of using these models to time series data to extend the generalized autoregressive moving average models discussed by Benjamin et al. [Generalized autoregressive moving average models. J. Amer. Statist. Assoc. 98, 214–223]. The usefulness of these models is illustrated in a simulation study and in applications to three real data sets.     

A counterexample to Beder's conjectures about Hadamard matrices

In this note we provide a counterexample which resolves conjectures about Hadamard matrices made in this journal. Beder [1998. Conjectures about Hadamard matrices. Journal of Statistical Planning and Inference 72, 7–14] conjectured that if H$\mathit{H}$ is a maximal m×n$m\times n$ row-Hadamard matrix then m is a multiple of 4; and that if n   is a power of 2 then every row-Hadamard matrix can be extended to a Hadamard matrix. Using binary integer programming we obtain a maximal 13×32$13\times 32$ row-Hadamard matrix, which disproves both conjectures. Additionally for n being a multiple of 4 up to 64, we tabulate values of m   for which we have found a maximal row-Hadamard matrix. Based on the tabulated results we conjecture that a m×n$m\times n$ row-Hadamard matrix with m?n-7$m?n-7$ can be extended to a Hadamard matrix.     

A new estimation method for Weibull-type tails based on the mean excess function

Studying the right tail of a distribution, one can classify the distributions into three classes based on the extreme value index γ$\gamma$. The class γ>0$\gamma >0$ corresponds to Pareto-type or heavy tailed distributions, while γ<0$\gamma <0$ indicates that the underlying distribution has a finite endpoint. The Weibull-type distributions form an important subgroup within the Gumbel class with γ=0$\gamma =0$. The tail behaviour can then be specified using the Weibull tail index. Classical estimators of this index show severe bias. In this paper we present a new estimation approach based on the mean excess function, which exhibits improved bias and mean squared error. The asserted properties are supported by simulation experiments and asymptotic results. Illustrations with real life data sets are provided.