On the use of diagnostic biplots in model screening for genotype by environment tables

Popular rank-2 and rank-3 models for two-way tables have geometrical properties which can be used as diagnostic keys in screening for an appropriate model. Row and column levels of two-way tables are represented by points in two or three dimensional space, whereupon collinearity and coplanarity of row and column points provide diagnostic keys for informal model choice. Coordinates are obtained from a factorization of the two-way table Y in the matrix product UV ^T. The rows of U then contain row-point coordinates and the rows of V column-point coordinates. Illustrations of applications of diagnostic biplots in the literature were restricted to data from chemistry and physics with little or no noise. In plant breeding, two-way tables containing substantial amounts of noise regularly arise in the form of genotype by environment tables. To investigate the usefulness of diagnostic biplots for model screening for genotype by environment tables, data tables were generated from a range of two-way models under the addition of various amounts of noise. Chances for correct diagnosis of the generating model depended on the type of model. Diagnostic biplots on their own do not seem to provide a sufficient means for model selection for genotype by environment tables, but in combination with other methods they certainly can provide extra insight into the structure of the data.     

A stratified estimation of a sensitive character by using geometric distribution

Abstract

In this paper, we consider the estimation of a sensitive character when the population is consisted of several strata; this is undertaken by applying Niharika et al.’s model which is using geometric distribution as a randomization device. A sensitive parameter is estimated for the case in which stratum size is known, and proportional and optimum allocation methods are taken into account. We extended the Niharika et al.’s model to the case of an unknown stratum size; a sensitive parameter is estimated by applying stratified double sampling to the Niharika et al.’s model. Finally, the efficiency of the proposed model is compared with that of Niharika et al. in terms of the estimator variance.     

Comparison of Selected Methods for Modeling of Multi-State Disease Progression Processes: A Simulation Study

Prognostic studies are essential to understand the role of particular prognostic factors and, thus, improve prognosis. In most studies, disease progression trajectories of individual patients may end up with one of mutually exclusive endpoints or can involve a sequence of different events.

One challenge in such studies concerns separating the effects of putative prognostic factors on these different endpoints and testing the differences between these effects.

In this article, we systematically evaluate and compare, through simulations, the performance of three alternative multivariable regression approaches in analyzing competing risks and multiple-event longitudinal data. The three approaches are: (1) fitting separate event-specific Cox's proportional hazards models; (2) the extension of Cox's model to competing risks proposed by Lunn and McNeil; and (3) Markov multi-state model.

The simulation design is based on a prognostic study of cancer progression, and several simulated scenarios help investigate different methodological issues relevant to the modeling of multiple-event processes of disease progression. The results highlight some practically important issues. Specifically, the decreased precision of the observed timing of intermediary (non fatal) events has a strong negative impact on the accuracy of regression coefficients estimated with either the Cox's or Lunn-McNeil models, while the Markov model appears to be quite robust, under the same circumstances. Furthermore, the tests based on both Markov and Lunn-McNeil models had similar power for detecting a difference between the effects of the same covariate on the hazards of two mutually exclusive events. The Markov approach yields also accurate Type I error rate and good empirical power for testing the hypothesis that the effect of a prognostic factor on changes after an intermediary event, which cannot be directly tested with the Lunn-McNeil method. Bootstrap-based standard errors improve the coverage rates for Markov model estimates. Overall, the results of our simulations validate Markov multi-state model for a wide range of data structures encountered in prognostic studies of disease progression, and may guide end users regarding the choice of model(s) most appropriate for their specific application.     

THE WRAPPED t FAMILY OF CIRCULAR DISTRIBUTIONS

This paper considers the three‐parameter family of symmetric unimodal distributions obtained by wrapping the location‐scale extension of Student's t distribution onto the unit circle. The family contains the wrapped normal and wrapped Cauchy distributions as special cases, and can be used to closely approximate the von Mises distribution. In general, the density of the family can only be represented in terms of an infinite summation, but its trigonometric moments are relatively simple expressions involving modified Bessel functions. Point estimation of the parameters is considered, and likelihood‐based methods are used to fit the family of distributions in an illustrative analysis of cross‐bed measurements. The use of the family as a means of approximating the von Mises distribution is investigated in detail, and new efficient algorithms are proposed for the generation of approximate pseudo‐random von Mises variates.     

Calculation Methods for Wallenius' Noncentral Hypergeometric Distribution

Two different probability distributions are both known in the literature as “the” noncentral hypergeometric distribution. Wallenius' noncentral hypergeometric distribution can be described by an urn model without replacement with bias. Fisher's noncentral hypergeometric distribution is the conditional distribution of independent binomial variates given their sum. No reliable calculation method for Wallenius' noncentral hypergeometric distribution has hitherto been described in the literature. Several new methods for calculating probabilities from Wallenius' noncentral hypergeometric distribution are derived. Range of applicability, numerical problems, and efficiency are discussed for each method. Approximations to the mean and variance are also discussed. This distribution has important applications in models of biased sampling and in models of evolutionary systems.     

Selection of regress or va riables when E(Y) is an unknown honlinear function

We consider the problem of deciding which of a set of p independent variables x₁ X₂J x_s we are to regard as being functionally involved in the mean of a dependent normal random variable Y and estimating E( Y) in terms of the chosen x's. This mean is an unknown function (assumed to be doubly differentiable) of some or all of the x's, so that the problem is of wide relevance. We approximate to the hypersurface in two different ways, and select within each approximation:

(a)For the situation where the mean of Y is assumed to be a linear function of the x's, we use ono of the optimum methods of selection.

(b)More generally, in the space of the X's the function will be approximately linear in a relatively small region. Accordingly this p-dimensional space is subdivided into smaller regions by a clustering procedure, and a hyperplane if fitted with in each region to aproximate to the unknown responce surface.An adaption of an optimum-regressor-selection procedure is then used to assist in the selection of the regressors

Approximate F tests are given to choose between models, including deciding how many x's to retain. Alternatively: the application of Akaike's Extended Maximum Likelihood Principle provides another way of choosing between the models and of selecting regressor variables. The methods are applied to data on glass manufacture.     

A novel approach to estimate the Cox model with temporal covariates and application to medical cost data

Abstract

We propose a novel approach to estimate the Cox model with temporal covariates. Our new approach treats the temporal covariates as arising from a longitudinal process which is modeled jointly with the event time. Different from the literature, the longitudinal process in our model is specified as a bounded variational process and determined by a family of Initial Value Problems associated with an Ordinary Differential Equation. Our specification has the advantage that only the observation of the temporal covariates at the event-time and the event-time itself are needed to fit the model, while it is fine but not necessary to have more longitudinal observations. This fact makes our approach very useful for many medical outcome datasets, such as the SPARCS and NIS, where it is important to find the hazard rate of being discharged given the accumulative cost but only the total cost at the discharge time is available due to the protection of private information. Our estimation procedure is based on maximizing the full information likelihood function. The resulting estimators are shown to be consistent and asymptotically normally distributed. Simulations and a real example illustrate the utility of the proposed model. Finally, a couple of extensions are discussed.     

Nonnull distribution of Wilks' statistic for Manova in the complex case

In this paper, the exact distribution of Wilks' likelihood ratio criterion, A, for MANOVA, in the complex case when the alternate hypothesis is of unit rank (i.e. the linear case) has been derived and the explicit expressions for the same for p = 2 and 3 (where p is the number of variates) and general f₁ (the error degrees of freedom) and f₂ (the hypothesis degrees of freedom), are given. For an unrestricted number of variables, a general form of the density and the distribution of A in this case, is also given. It has been shown that the total integral of the series obtained by taking a few terms only, rapidly approaches the theoretical value one as more terms are taken into account, and some percentage points have also been computed.     

INFLUENTIAL OBSERVATION IDENTIFICATION IN THE GROWTH CURVE MODEL WITH RAO'S SIMPLE COVARIANCE STRUCTURE

ABSTRACT

In this paper we discuss the identification of influential observations in a growth curve model with Rao's simple covariance structure. Based on the generalized Cook-type distance and the volume of a confidence ellipsoid, a variety of influence measures are proposed in terms of the case-deletion technique. Also, the influence of observations on a linear combination of regression coefficients is considered. For illustration, a practical example is analyzed using the proposed approach.     

Simulation from the bessel distribution with applications

The Bessel distribution, introduced recently by Yuan and Kalbfleisch (Ann. Inst. Math. Statist., 2000), can be useful in many applications. In particular, this distribution appears in two Bayesian estimation problems, namely, estimation of the noncentrality parameter of a noncentral chi-square distribution and of the parameters of Downton's bivariate exponential distribution. Implementation of Markov chain Monte Carlo algorithms requires generation of observations from the Bessel distribution. In this paper we propose and compare exact simulation schemes generating Bessel variates based on certain properties of the distribution as well as the rejection method.     

Role of weights in improving the efficiency of Kim and Warde's mixed randomized response model

ABSTARCT

In this paper we have suggested a class of unbiased estimators of π_S, the proportion of respondents possessing a sensitive attribute A using mixed randomized response model. The variance of the proposed class of estimators has been obtained. In addition to Kim and Warde's (2005) estimator, several other acceptable estimators of π_S have been identified from the proposed class for suitable weights. It has been shown that the newly identified estimators are more efficient than the Kim and Warde's (2005) estimator. Numerical illustrations and graphs are also given in support of the present study.     

COMPARING TESTS OF AUTOREGRESSIVE VERSUS MOVING AVERAGE ERRORS IN REGRESSION MODELS USING BAHADUR’S ASYMPTOTIC RELATIVE EFFICIENCY

ABSTRACT

The purpose of this paper is to use Bahadur's asymptotic relative efficiency measure to compare the performance of various tests of autoregressive (AR) versus moving average (MA) error processes in regression models. Tests to be examined include non-nested procedures of the models against each other, and classical procedures based upon testing both the AR and MA error processes against the more general autoregressive-moving average model.     

Tests for detecting overdispersion in poisson models

Collings and Margolin(1985) developed a locally most powerful unbiased test for detecting negative binomial departures from a Poisson model, when the variance is a quadratic function of the mean. Kim and Park(1992) developed a locally most powerful unbiased test, when the variance is a linear function of the mean. It is found that a different mean-variance structure of a negative binomial derives a different locally optimal test statistic.

In this paper Collings and Margolin's and Kim and Park's results are unified and extended by developing a test for overdispersion in Poisson model against Katz family of distributions, Our setup has two extensions: First, Katz family of distributions is employed as an extension of the negative binomial distribution. Second, the mean-variance structure of the mixed Poisson model is given by σ² = μ+cμ^r for arbitrary but fixed r. We derive a local score test for testing H₀ : c = 0. Superiority of a new test is proved by the asymtotic relative efficiency as well as the simulation study.     

Spatial Mallows model averaging for geostatistical models

Important progress has been made with model averaging methods over the past decades. For spatial data, however, the idea of model averaging has not been applied well. This article studies model averaging methods for the spatial geostatistical linear model. A spatial Mallows criterion is developed to choose weights for the model averaging estimator. The resulting estimator can achieve asymptotic optimality in terms of L₂ loss. Simulation experiments reveal that our proposed estimator is superior to the model averaging estimator by the Mallows criterion developed for ordinary linear models [Hansen, 2007] and the model selection estimator using the corrected Akaike's information criterion, developed for geostatistical linear models [Hoeting et al., 2006]. The Canadian Journal of Statistics 47: 336–351; 2019 © 2019 Statistical Society of Canada     

A SINful approach to Gaussian graphical model selection

Multivariate Gaussian graphical models are defined in terms of Markov properties, i.e., conditional independences, corresponding to missing edges in the graph. Thus model selection can be accomplished by testing these independences, which are equivalent to zero values of corresponding partial correlation coefficients. For concentration graphs, acyclic directed graphs, and chain graphs (both LWF and AMP classes), we apply Fisher's z-transform, Šidák's correlation inequality, and Holm's step-down procedure to simultaneously test the multiple hypotheses specified by these zero values. This simple method for model selection controls the overall error rate for incorrect edge inclusion. Prior information about the presence and/or absence of particular edges can be readily incorporated.     

Model averaging by jackknife criterion for varying-coefficient partially linear models

Abstract

This paper is concerned with model averaging procedure for varying-coefficient partially linear models. We proposed a jackknife model averaging method that involves minimizing a leave-one-out cross-validation criterion, and developed a computational shortcut to optimize the cross-validation criterion for weight choice. The resulting model average estimator is shown to be asymptotically optimal in terms of achieving the smallest possible squared error. The simulation studies have provided evidence of the superiority of the proposed procedures. Our approach is further applied to a real data.     

Post model-fitting exploration via a “Next-Door” analysis

We propose a simple method for evaluating the model that has been chosen by an adaptive regression procedure, our main focus being the lasso. This procedure deletes each chosen predictor and refits the lasso to get a set of models that are “close” to the chosen “base model,” and compares the error rates of the base model with that of nearby models. If the deletion of a predictor leads to significant deterioration in the model's predictive power, the predictor is called indispensable; otherwise, the nearby model is called acceptable and can serve as a good alternative to the base model. This provides both an assessment of the predictive contribution of each variable and a set of alternative models that may be used in place of the chosen model. We call this procedure “Next-Door analysis” since it examines models “next” to the base model. It can be applied to supervised learning problems with ℓ₁ penalization and stepwise procedures. We have implemented it in the R language as a library to accompany the well-known glmnet library. The Canadian Journal of Statistics 48: 447–470; 2020 © 2020 Statistical Society of Canada     

Randomized response model versus mixture model in the crossover design for clinical trials

ABSTRACT

The clinical trials are usually designed with the implicit assumption that data analysis will occur only after the trial is completed. It is a challenging problem if the sponsor wishes to evaluate the drug efficacy in the middle of the study without breaking the randomization codes. In this article, the randomized response model and mixture model are introduced to analyze the data, masking the randomization codes of the crossover design. Given the probability of treatment sequence, the test of mixture model provides higher power than the test of randomized response model, which is inadequate in the example. The paired t-test has higher powers than both models if the randomization codes are broken. The sponsor may stop the trial early to claim the effectiveness of the study drug if the mixture model concludes a positive result.     

On approximations to the inverse student’s-t distribution function

The inverse of the Student's t-distribution is often needed in computer simulation and applied statistics, e.g, in generating random variates from t-distributions and in computing tables needed for statistical procedures which do not assume known variances. The t-distribution algorithm of Dudewicz and Dalal (1972) can be used to approximate the inverset t distribution function. The author notes an algorithm for evaluation of this inverse d.f. which can be implemented in a fast, accurate and short computer program. The error analysis is also reported. An application is considered for the problem of testing the hypothesis that a sequence of random variates follows Student's-t distribution.     

Control Variates for Monte Carlo Analysis of Nonlinear Statistical Models,I: Overview

Parameter values of nonlinear statistical models are typically estimated from data using iterative numerical procedures. The resulting joint sampling distribution of the parameter estimators is often intractable, resulting in the use of approximators or Monte Carlo simulation to determine properties of the sampling distribution.

This paper develops methods, using linear and higher-order approximators as control variates that reduce the variance of the Monte Carlo estimator by orders of magnitude. Estimation of means, higher-order raw moments, variances, covariances, and percentiles is considered.