Large sample interval mapping method for genetic trait loci in finite regression mixture models

This article investigates the large sample interval mapping method for genetic trait loci (GTL) in a finite non-linear regression mixture model. The general model includes most commonly used kernel functions, such as exponential family mixture, logistic regression mixture and generalized linear mixture models, as special cases. The populations derived from either the backcross or intercross design are considered. In particular, unlike all existing results in the literature in the finite mixture models, the large sample results presented in this paper do not require the boundness condition on the parametric space. Therefore, the large sample theory presented in this article possesses general applicability to the interval mapping method of GTL in genetic research. The limiting null distribution of the likelihood ratio test statistics can be utilized easily to determine the threshold values or p-values required in the interval mapping. The limiting distribution is proved to be free of the parameter values of null model and free of the choice of a kernel function. Extension to the multiple marker interval GTL detection is also discussed. Simulation study results show favorable performance of the asymptotic procedure when sample sizes are moderate.     

Estimating the distribution function using k-tuple ranked set samples

The basic assumption underlying the concept of ranked set sampling is that actual measurement of units is expensive, whereas ranking is cheap. This may not be true in reality in certain cases where ranking may be moderately expensive. In such situations, based on total cost considerations, k-tuple ranked set sampling is known to be a viable alternative, where one selects k units (instead of one) from each ranked set. In this article, we consider estimation of the distribution function based on k-tuple ranked set samples when the cost of selecting and ranking units is not ignorable. We investigate estimation both in the balanced and unbalanced data case. Properties of the estimation procedure in the presence of ranking error are also investigated. Results of simulation studies as well as an application to a real data set are presented to illustrate some of the theoretical findings.     

Statistical inference for a general class of asymmetric distributions

We consider a general class of asymmetric univariate distributions depending on a real-valued parameter α, which includes the entire family of univariate symmetric distributions as a special case. We discuss the connections between our proposal and other families of skew distributions that have been studied in the statistical literature. A key element in the construction of such families of distributions is that they can be stochastically represented as the product of two independent random variables. From this representation we can readily derive theoretical properties, easy-to-implement simulation schemes as well as extensions to the multivariate case. We also study statistical inference for this class based on the method of moments and maximum likelihood. We give special attention to the skew-power exponential distribution, but other cases like the skew-t distribution are also considered. Finally, the statistical methods are illustrated with 3 examples based on real datasets.     

Inference of non-centrality parameter of a truncated non-central chi-squared distribution

Non-central chi-squared distribution plays a vital role in statistical testing procedures. Estimation of the non-centrality parameter provides valuable information for the power calculation of the associated test. We are interested in the statistical inference property of the non-centrality parameter estimate based on one observation (usually a summary statistic) from a truncated chi-squared distribution. This work is motivated by the application of the flexible two-stage design in case–control studies, where the sample size needed for the second stage of a two-stage study can be determined adaptively by the results of the first stage. We first study the moment estimate for the truncated distribution and prove its existence, uniqueness, and inadmissibility and convergence properties. We then define a new class of estimates that includes the moment estimate as a special case. Among this class of estimates, we recommend to use one member that outperforms the moment estimate in a wide range of scenarios. We also present two methods for constructing confidence intervals. Simulation studies are conducted to evaluate the performance of the proposed point and interval estimates.     

Some bounds on balanced block designs

Bounds on the latest root of the C-matrix and the number of blocks for a variance-balanced block design are given. These results contain the well-known results as special cases.     

Second order asymptotic and non-asymptotic optimality properties of combined tests

Let p independent test statistics be available to test a null hypothesis concerned with the same parameter. The p are assumed to be similar tests. Asymptotic and non-asymptotic optimality properties of combined tests are studied. The asymptotic study centers around two notions. The first is Bahadur efficiency. The second is based on a notion of second order comparisons. The non-asymptotic study is concerned with admissibility questions. Most of the popular combining methods are considered along with a method not studied in the past. Among the results are the following: Assume each of the p statistics has the same Bahadur slope. Then the combined test based on the sum of normal transforms, is asymptotically best among all tests studied, by virtue of second order considerations. Most of the popular combined tests are inadmissible for testing the noncentrality parameter of chi-square, t, and F distributions. For chi-square a combined test is offered which is admissible, asymptotically optimal (first order), asymptotically optimal (second order) among all tests studied, and for which critical values are obtainable in special cases. Extensions of the basic model are given.     

Efficiency of weighted averages

When combining estimates of a common parameter (of dimension d?1$d?1$) from independent data sets—as in stratified analyses and meta analyses—a weighted average, with weights ‘proportional’ to inverse variance matrices, is shown to have a minimal variance matrix (a standard fact when d=1$d=1$)—minimal in the sense that all convex combinations of the coordinates of the combined estimate have minimal variances. Minimum variance for the estimation of a single coordinate of the parameter can therefore be achieved by joint estimation of all coordinates using matrix weights. Moreover, if each estimate is asymptotically efficient within its own data set, then this optimally weighted average, with consistently estimated weights, is shown to be asymptotically efficient in the combined data set and avoids the need to merge the data sets and estimate the parameter in question afresh. This is so whatever additional non-common nuisance parameters may be in the models for the various data sets. A special case of this appeared in Fisher [1925. Theory of statistical estimation. Proc. Cambridge Philos. Soc. 22, 700–725.]: Optimal weights are ‘proportional’ to information matrices, and he argued that sample information should be used as weights rather than expected information, to maintain second-order efficiency of maximum likelihood. A number of special cases have appeared in the literature; we review several of them and give additional special cases, including stratified regression analysis—proportional-hazards, logistic or linear—, combination of independent ROC curves, and meta analysis. A test for homogeneity of the parameter across the data sets is also given.     

Asymptotics for tests on mean profiles,additional information and dimensionality under non-normality

We consider the comparison of mean vectors for k groups when k is large and sample size per group is fixed. The asymptotic null and non-null distributions of the normal theory likelihood ratio, Lawley–Hotelling and Bartlett–Nanda–Pillai statistics are derived under general conditions. We extend the results to tests on the profiles of the mean vectors, tests for additional information (provided by a sub-vector of the responses over and beyond the remaining sub-vector of responses in separating the groups) and tests on the dimension of the hyperplane formed by the mean vectors. Our techniques are based on perturbation expansions and limit theorems applied to independent but non-identically distributed sequences of quadratic forms in random matrices. In all these four MANOVA problems, the asymptotic null and non-null distributions are normal. Both the null and non-null distributions are asymptotically invariant to non-normality when the group sample sizes are equal. In the unbalanced case, a slight modification of the test statistics will lead to asymptotically robust tests. Based on the robustness results, some approaches for finite approximation are introduced. The numerical results provide strong support for the asymptotic results and finiteness approximations.     

Flexible univariate and multivariate models based on hidden truncation

A broad spectrum of flexible univariate and multivariate models can be constructed by using a hidden truncation paradigm. Such models can be viewed as being characterized by a basic marginal density, a family of conditional densities and a specified hidden truncation point, or points. The resulting class of distributions includes the basic marginal density as a special case (or as a limiting case), but also includes an array of models that may unexpectedly include many well known densities. Most of the well known skew-normal models (developed from the seed distribution popularized by Azzalini [(1985). A class of distributions which includes the normal ones. Scand. J. Statist. 12(2), 171–178]) can be viewed as being products of such a hidden truncation construction. However, the many hidden truncation models with non-normal component densities undoubtedly deserve further attention.     

Flexible mixture modelling using the multivariate skew-t-normal distribution

This paper presents a robust probabilistic mixture model based on the multivariate skew-t-normal distribution, a skew extension of the multivariate Student’s t distribution with more powerful abilities in modelling data whose distribution seriously deviates from normality. The proposed model includes mixtures of normal, t and skew-normal distributions as special cases and provides a flexible alternative to recently proposed skew t mixtures. We develop two analytically tractable EM-type algorithms for computing maximum likelihood estimates of model parameters in which the skewness parameters and degrees of freedom are asymptotically uncorrelated. Standard errors for the parameter estimates can be obtained via a general information-based method. We also present a procedure of merging mixture components to automatically identify the number of clusters by fitting piecewise linear regression to the rescaled entropy plot. The effectiveness and performance of the proposed methodology are illustrated by two real-life examples.     

A p-value for testing the equivalence of the variances of a bivariate normal distribution

A p-value is developed for testing the equivalence of the variances of a bivariate normal distribution. The unknown correlation coefficient is a nuisance parameter in the problem. If the correlation is known, the proposed p-value provides an exact test. For large samples, the p-value can be computed by replacing the unknown correlation by the sample correlation, and the resulting test is quite satisfactory. For small samples, it is proposed to compute the p-value by replacing the unknown correlation by a scalar multiple of the sample correlation. However, a single scalar is not satisfactory, and it is proposed to use different scalars depending on the magnitude of the sample correlation coefficient. In order to implement this approach, tables are obtained providing sub-intervals for the sample correlation coefficient, and the scalars to be used if the sample correlation coefficient belongs to a particular sub-interval. Once such tables are available, the proposed p-value is quite easy to compute since it has an explicit analytic expression. Numerical results on the type I error probability and power are reported on the performance of such a test, and the proposed p-value test is also compared to another test based on a rejection region. The results are illustrated with two examples: an example dealing with the comparability of two measuring devices, and an example dealing with the assessment of bioequivalence.     

Nonparametric methods in multivariate factorial designs for large number of factor levels

We propose different multivariate nonparametric tests for factorial designs and derive their asymptotic distribution for the situation where the number of replications is limited, whereas the number of treatments goes to infinity (large a, small n case). The tests are based on separate rankings for the different variables, and they are therefore invariant under separate monotone transformations of the individual variables.     

A systematic review on model selection in high-dimensional regression

High dimensional models are getting much attention from diverse research fields involving very many parameters with a moderate size of data. Model selection is an important issue in such a high dimensional data analysis. Recent literature on theoretical understanding of high dimensional models covers a wide range of penalized methods including LASSO and SCAD. This paper presents a systematic overview of the recent development in high dimensional statistical models. We provide a brief review on the recent development of theory, methods, and guideline on applications of several penalized methods. The review includes appropriate settings to be implemented and limitations along with potential solution for each of the reviewed method. In particular, we provide a systematic review of statistical theory of the high dimensional methods by considering a unified high-dimensional modeling framework together with high level conditions. This framework includes (generalized) linear regression and quantile regression as its special cases. We hope our review helps researchers in this field to have a better understanding of the area and provides useful information to future study.     

Horvitz-Thompson estimator and generalized πPS designs

Generalized πPS designs were defined by T.J. Rao (1972). Working with a general super-population model θ(g), the strategy consisting of GπPS design together with the associated Horvitz-Thompson estimator of the population total was shown to be better than two other well known strategies in T.J. Rao (1971,1972). In this note we prove the θ(g)-optimality of the strategy consisting of GπPS design together with the associated Horvitz-Thompson estimator in the entire class of p-unbiased strategies of the population total with expected sample size fixed. In view of our theorem the results of T.J. Rao follow as special cases.     

Characteristic function estimation of non-Gaussian Ornstein–Uhlenbeck processes

Continuous non-Gaussian stationary processes of the OU-type are becoming increasingly popular given their flexibility in modelling stylized features of financial series such as asymmetry, heavy tails and jumps. The use of non-Gaussian marginal distributions makes likelihood analysis of these processes unfeasible for virtually all cases of interest. This paper exploits the self-decomposability of the marginal laws of OU processes to provide explicit expressions of the characteristic function which can be applied to several models as well as to develop efficient estimation techniques based on the empirical characteristic function. Extensions to OU-based stochastic volatility models are provided.     

The Bernstein–von Mises theorem in semiparametric competing risks models

Semiparametric Bayesian models are nowadays a popular tool in event history analysis. An important area of research concerns the investigation of frequentist properties of posterior inference. In this paper, we propose novel semiparametric Bayesian models for the analysis of competing risks data and investigate the Bernstein–von Mises theorem for differentiable functionals of model parameters. The model is specified by expressing the cause-specific hazard as the product of the conditional probability of a failure type and the overall hazard rate. We take the conditional probability as a smooth function of time and leave the cumulative overall hazard unspecified. A prior distribution is defined on the joint parameter space, which includes a beta process prior for the cumulative overall hazard. We first develop the large-sample properties of maximum likelihood estimators by giving simple sufficient conditions for them to hold. Then, we show that, under the chosen priors, the posterior distribution for any differentiable functional of interest is asymptotically equivalent to the sampling distribution derived from maximum likelihood estimation. A simulation study is provided to illustrate the coverage properties of credible intervals on cumulative incidence functions.     

Parsimonious Gaussian mixture models

Parsimonious Gaussian mixture models are developed using a latent Gaussian model which is closely related to the factor analysis model. These models provide a unified modeling framework which includes the mixtures of probabilistic principal component analyzers and mixtures of factor of analyzers models as special cases. In particular, a class of eight parsimonious Gaussian mixture models which are based on the mixtures of factor analyzers model are introduced and the maximum likelihood estimates for the parameters in these models are found using an AECM algorithm. The class of models includes parsimonious models that have not previously been developed. These models are applied to the analysis of chemical and physical properties of Italian wines and the chemical properties of coffee; the models are shown to give excellent clustering performance.     

Some locally optimal subset selection rules for comparison with a control

Let π₀,π₁,…,π_k be k+1 independent populations. For i=0,1,…,k,π_i has the densit f(x,θ_i), where the (unknown) parameter θ_i belongs to an interval of the real line. Our goal is to select from π₁,… π_k (experimental treatments) those populations, if any, that are better (suitably defined) than π₀ which is the control population. A locally optimal rule is derived in the class of rules for which Pr(π_i is selected)γ_i, i=1,…,k, when θ₀=θ₁=?=θ_k. The criterion used for local optimality amounts to maximizing the efficiency in a certain sense of the rule in picking out the superior populations for specific configurations of θ=(θ₀,…,θ_k) in a neighborhood of an equiparameter configuration. The general result is then applied to the following special cases: (a) normal means comparison — common known variance, (b) normal means comparison — common unknown variance, (c) gamma scale parameters comparison — known (unequal) shape parameters, and (d) comparison of regression slopes. In all these cases, the rule is obtained based on samples of unequal sizes.     

Designs for cropping systems research

The present article establishes equivalence between extended group divisible (EGD) designs and designs for crop sequence experiments. This equivalence has encouraged the agricultural experimenters to use EGD designs for their experimentation. Some real life applications of EGD designs have been given. It has also been shown that several existing association schemes are special cases of EGD association scheme. Some methods of construction of EGD designs are also given. A catalogue of EGD designs obtainable through methods of construction along with efficiency factors of various factorial effects is also presented. In some crop sequence experiments that are conducted to develop suitable integrated nutrient supply system of a crop sequence, the treatments do not comprise of a complete factorial structure. The experimenter is interested in estimating the residual and direct effect of the treatments along with their cumulative effects. For such experimental settings block designs with two sets of treatments applied in succession are the appropriate designs. The correspondence established between row–column designs and block designs for two stage experiments by Parsad et al. [2003. Structurally incomplete row–column designs. Comm. Statist. Theory Methods 32(1), 239–261] has been exploited in obtaining designs for such experimental situations. Some open problems related to designing of crop sequence experiments are also given.     

Nonparametric hierarchical Bayes analysis of binomial data via Bernstein polynomial priors

For binomial data analysis, many methods based on empirical Bayes interpretations have been developed, in which a variance‐stabilizing transformation and a normality assumption are usually required. To achieve the greatest model flexibility, we conduct nonparametric Bayesian inference for binomial data and employ a special nonparametric Bayesian prior—the Bernstein–Dirichlet process (BDP)—in the hierarchical Bayes model for the data. The BDP is a special Dirichlet process (DP) mixture based on beta distributions, and the posterior distribution resulting from it has a smooth density defined on [0, 1]. We examine two Markov chain Monte Carlo procedures for simulating from the resulting posterior distribution, and compare their convergence rates and computational efficiency. In contrast to existing results for posterior consistency based on direct observations, the posterior consistency of the BDP, given indirect binomial data, is established. We study shrinkage effects and the robustness of the BDP‐based posterior estimators in comparison with several other empirical and hierarchical Bayes estimators, and we illustrate through examples that the BDP‐based nonparametric Bayesian estimate is more robust to the sample variation and tends to have a smaller estimation error than those based on the DP prior. In certain settings, the new estimator can also beat Stein's estimator, Efron and Morris's limited‐translation estimator, and many other existing empirical Bayes estimators. The Canadian Journal of Statistics 40: 328–344; 2012 © 2012 Statistical Society of Canada