Two Statistics for Unconditional Exact Tests in Matched-Pairs Design

Abstract

In a recent article Hsueh et al. (Hsueh, H.-M., Liu, J.-P., Chen, J. J. (2001 Hsueh, H.-M., Liu, J.-P. and Chen, J. J. 2001. Unconditional exact tests for equivalence or noninferiority for paired binary endpoints. Biometrics, 57: 478–483. [Crossref], [PubMed], [Web of Science ®] , [Google Scholar]). Unconditional exact tests for equivalence or noninferiority for paired binary endpoints. Biometrics 57:478–483.) considered unconditional exact tests for paired binary endpoints. They suggested two statistics one of which is based on the restricted maximum-likelihood estimator. Properties of these statistics and the related tests are treated in this article.     

Choosing Ridge Parameter for Regression Problems

ABSTRACT

Hoerl and Kennard (1970a Hoerl , A. E. , Kennard , R. W. ( 1970a ). Ridge regression: biased estimation for non-orthogonal problems . Tech. 12 : 55 – 67 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) introduced the ridge regression estimator as an alternative to the ordinary least squares estimator in the presence of multicollinearity. In this article, a new approach for choosing the ridge parameter (K), when multicollinearity among the columns of the design matrix exists, is suggested and evaluated by simulation techniques, in terms of mean squared errors (MSE). A number of factors that may affect the properties of these methods have been varied. The MSE from this approach has shown to be smaller than using Hoerl and Kennard (1970a Hoerl , A. E. , Kennard , R. W. ( 1970a ). Ridge regression: biased estimation for non-orthogonal problems . Tech. 12 : 55 – 67 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) in almost all situations.     

MODIFICATION OF KELLY AND RICE METHOD FOR SYNERGISM TESTS

ABSTRACT

In this paper, we present a modified Kelly and Rice method for testing synergism. This approach is consistent with Berenbaum's1-3 Berenbaum, M.C. 1977. Synergism, Additivism, and Antagonism in Immuno-Suppression: A Critical Review. Clinical and Experimental Immunology, 28: 1–18. Berenbaum, M.C. 1985. The Expected Effect of a Combination of Agents: The General Solution. Journal of Theoretical Biology, 114: 413–431. Berenbaum, M.C. 1989. What is Synergism? Pharmacological Reviews. 41: 93–141.   framework for additivity. The delta method[4] Bishop, Y.M., Fienberg, S.E. and Holland, P.W. 1975. Discrete Multivariate Analysis: Theory and Practice Massachusetts: MIT Press.  [Google Scholar] is applied to obtain the estimated variance for the predicted additivity proportion. A Monte Carlo simulation study for the evaluation of the method's performance, i.e., global overall tests for synergism, is also discussed. Kelly and Rice[5] Kelly, C. and Rice, J. 1990. Monotone Smoothing with Application to Dose-Response Curves and the Assessment of Synergism. Biometrics, 46: 1071–1085. [Crossref], [PubMed], [Web of Science ®] , [Google Scholar] do not provide a correct test statistic because the variance is underestimated. Hence, the performance of the Kelly–Rice[5] Kelly, C. and Rice, J. 1990. Monotone Smoothing with Application to Dose-Response Curves and the Assessment of Synergism. Biometrics, 46: 1071–1085. [Crossref], [PubMed], [Web of Science ®] , [Google Scholar] method is generally anti-conservative, based on the simulation findings. In addition, the overall test of synergism with χ²(r) from the modified Kelly and Rice method for larger sample sizes is better than that with χ²(1) from the modified Kelly and Rice method.     

MULTI-LEVEL FACTORIAL DESIGNS WITH MINIMUM NUMBERS OF LEVEL CHANGES

The order of experimental runs in a fractional factorial experiment is essential when the cost of level changes in factors is considered. The generalized foldover scheme given by [1] Coster, D. C. and Cheng, C. S. 1988. Minimum cost trend free run orders of fractional factorial designs. The Annals of Statistics, 16: 1188–1205. [Crossref], [Web of Science ®] , [Google Scholar]gives an optimal order to experimental runs in an experiment with specified defining contrasts. An experiment can be specified by a design requirement such as resolution or estimation of some interactions. To meet such a requirement, we can find several sets of defining contrasts. Applying the generalized foldover scheme to these sets of defining contrasts, we obtain designs with different numbers of level changes and then the design with minimum number of level changes. The difficulty is to find all the sets of defining contrasts. An alternative approach is investigated by [2] Cheng, C. S., Martin, R. J. and Tang, B. 1998. Two-level factorial designs with extreme numbers of level changes. The Annals of Statistics, 26: 1522–1539. [Crossref], [Web of Science ®] , [Google Scholar]for two-level fractional factorial experiments. In this paper, we investigate experiments with all factors in slevels.     

A Class of Improved Heteroskedasticity-Consistent Covariance Matrix Estimators

Abstract

The heteroskedasticity-consistent covariance matrix estimator proposed by White [White, H. A. (1980 White, H. A. 1980. Heteroskedasticity-consistent covariance matrix estimator and a direct test for heteroskedasticity. Econometrica, 48: 817–838. [Crossref], [Web of Science ®] , [Google Scholar]). Heteroskedasticity-consistent covariance matrix estimator and a direct test for heteroskedasticity. Econometrica 48:817–838], also known as HC0, is commonly used in practical applications and is implemented into a number of statistical software. Cribari–Neto et al. [Cribari–Neto, F., Ferrari, S. L. P., Cordeiro, G. M. (2000 Cribari–Neto, F., Ferrari, S. L. P. and Cordeiro, G. M. 2000. Improved heteroscedasticity–consistent covariance matrix estimators. Biometrika, 87: 907–918. [Crossref], [Web of Science ®] , [Google Scholar]). Improved heteroscedasticity–consistent covariance matrix estimators. Biometrika 87:907–918] have developed a bias-adjustment scheme that delivers bias-corrected White estimators. There are several variants of the original White estimator that are also commonly used by practitioners. These include the HC1, HC2, and HC3 estimators, which have proven to have superior small-sample behavior relative to White's estimator. This paper defines a general bias-correction mechamism that can be applied not only to White's estimator, but to variants of this estimator as well, such as HC1, HC2, and HC3. Numerical evidence on the usefulness of the proposed corrections is also presented. Overall, the results favor the sequence of improved HC2 estimators.     

Automatic Smoothing for Poisson Regression

Abstract

Adaptive choice of smoothing parameters for nonparametric Poisson regression (O'Sullivan et al., 1986 O'Sullivan , F. , Yandell , B. S. , Raynor , W. J., Jr. ( 1986 ). Automatic smoothing of regression functions in generalized linear models . J. Amer. Statist. Assoc. 81 : 96 – 103 . [CSA] [Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) is considered in this article. A computable approximation of the unbiased risk estimate (AUBR) for Poisson regression is introduced. This approximation can be used to automatically tune the smoothing parameter for the penalized likelihood estimator. An alternative choice is the generalized approximate cross validation (GACV) proposed by Xiang and Wahba (1996 Xiang , D. , Wahba , G. ( 1996 ). A generalized approximate cross validation for smoothing splines with non-Gaussian data . Statist. Sinica 6 (3): 675 – 692 .[Web of Science ®] , [Google Scholar]). Although GACV enjoys a great success in practice when applying for nonparametric logisitic regression, its performance for Poisson regression is not clear. Numerical simulations have been conducted to evaluate the GACV and AUBR based tuning methods. We found that GACV has a tendency to oversmooth the data when the intensity function is small. As a consequence, we suggest tuning the smoothing parameter using AUBR in practice.     

Skewing and Generalized Jackknifing in Kernel Density Estimation

Abstract

Kernel methods are very popular in nonparametric density estimation. In this article we suggest a simple estimator which reduces the bias to the fourth power of the bandwidth, while the variance of the estimator increases only by at most a moderate constant factor. Our proposal turns out to be a fourth order kernel estimator and may be regarded as a new version of the generalized jackknifing approach (Schucany W. R., Sommers, J. P. (1977 Schucany, W. R. and Sommers, J. P. 1977. Improvement of kernel type estimators. Journal of the American Statistical Association, 72: 420–423. [Taylor & Francis Online], [Web of Science ®] , [Google Scholar]). Improvement of Kernal type estimators. Journal of the American Statistical Association 72:420–423.) applied to kernel density estimation.     

A NEW VERSION OF THE LOCAL CONSTANT M-SMOOTHER

ABSTRACT

In the case of the equally spaced fixed design nonparametric regression, the local constant M-smoother (LCM) in Chu, Glad, Godtliebsen, and Marron [1] Chu, C.K., Glad, I., Godtliebsen, F. and Marron, J.S. 1998. Edge-Preserving Smoothers for Image Processing (with discussion). Journal of the American Statistical Association, 93: 526–556. [Taylor & Francis Online], [Web of Science ®] , [Google Scholar] has the interesting property of jump-preserving. However, it suffers from the problem of boundary effects. To correct for such adverse effects on the LCM, Rue, Chu, Godtliebsen, and Marron [2] Rue, H., Chu, C.K., Godtliebsen, F. and Marron, J.S. 2001. M-smoother with Local Linear Fit. To appear in Journal of Nonparametric Statistics [Google Scholar] apply the local linear fit to the “inside” of the kernel function, and propose the local linear M-smoother (LLM). Unfortunately, the LLM is more sensitive to random fluctuations, since an extra tuning parameter is included. To avoid such a practical drawback to the LLM, we propose a new version of the LCM by applying the local linear fit to the “outside” of the kernel function. Our proposed estimator employs both the same tuning parameter associated with the ordinary LCM and the same weights assigned to the observations by the local linear smoother in Fan 3-4 Fan, J. 1992. Design-adaptive Nonparametric Regression. Journal of the American Statistical Association, 87: 998–1004. Fan, J. 1993. Local Linear Regression Smoothers and Their Minimax Efficiencies. Annals of Statistics, 21: 196–216.  . It has the same asymptotic mean square error as the LLM. In practice, it can be calculated by using the fast computation algorithm designed for the ordinary LCM by Chu et al. [1] Chu, C.K., Glad, I., Godtliebsen, F. and Marron, J.S. 1998. Edge-Preserving Smoothers for Image Processing (with discussion). Journal of the American Statistical Association, 93: 526–556. [Taylor & Francis Online], [Web of Science ®] , [Google Scholar], and does not suffer from the drawback to the LLM. More importantly, our results obtained for the new version of the LCM in the one-dimensional case can be extended directly to the multidimensional case. Simulation studies demonstrate that the asymptotic effects hold for reasonable sample sizes.     

A Comparison of Procedures for Controlling the False Discovery Rate in the Presence of Small Variance Genes: A Simulation Study

The Significance Analysis of Microarrays (SAM; Tusher et al., 2001 Tusher , V. G. , Tibshirani , R. , Chu , G. ( 2001 ). Significance analysis of microarrys applied to the ionizing radiation response . Proceedings of the National Academy of Sciences 98 : 5116 – 5121 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]) method is widely used in analyzing gene expression data while controlling the FDR by using resampling-based procedure in the microarray setting. One of the main components of the SAM procedure is the adjustment of the test statistic. The introduction of the fudge factor to the test statistic aims at deflating the large value of test statistics due to the small standard error of gene-expression. Lin et al. (2008 Lin , D. , Shkedy , Z. , Burzykowski , T. , Göhlmann , H. W. H. , De Bondt , A. , Perera , T. , Geerts , T. , Bijnens , L. ( 2008 ). Significance analysis of microarray (SAM) for comparisons of several treatments with one control . Biometric Journal, MCP 50 ( 5 ): 801 – 823 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]) pointed out that the fudge factor does not effectively improve the power and the control of the FDR as compared to the SAM procedure without the fudge factor in the presence of small variance genes. Motivated by the simulation results presented in Lin et al. (2008 Lin , D. , Shkedy , Z. , Burzykowski , T. , Göhlmann , H. W. H. , De Bondt , A. , Perera , T. , Geerts , T. , Bijnens , L. ( 2008 ). Significance analysis of microarray (SAM) for comparisons of several treatments with one control . Biometric Journal, MCP 50 ( 5 ): 801 – 823 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]), in this article, we extend our study to compare several methods for choosing the fudge factor in the modified t-type test statistics and use simulation studies to investigate the power and the control of the FDR of the considered methods.     

The Product-Limit Estimate as an Inverse-Probability-Weighted Average

Abstract

For randomly censored data, (Satten, G. A., Datta S. (2001 Satten, G. A. and Datta, S. 2001. The Kaplan–Meier estimator as an inverse-probability-of-censoring weighted average. Amer. Statist. Ass., 55: 207–210. [Taylor & Francis Online], [Web of Science ®] , [Google Scholar]). The Kaplan–Meier estimator as an inverse-probability-of-censoring weighted average. Amer. Statist. Ass. 55:207–210) showed that the Kaplan–Meier estimator (product-limit estimator (PLE)) can be expressed as an inverse-probability-weighted average. In this article, we consider the other two PLEs: the truncation PLE and the censoring-truncation PLE. For the data subject to left-truncation or both left-truncation and right-censoring, it is shown that these two PLEs can be expressed as inverse-probability-weighted averages.     

RAO'S STATISTIC FOR THE ANALYSIS OF UNIFORM ASSOCIATION IN CROSS-CLASSIFICATIONS

In this paper we introduce a new measure for the analysis of association in cross-classifications having ordered categories. Association is measured in terms of the odd-ratios in 2 × 2 subtables formed from adjacent rows and adjacent columns. We focus our attention in the uniform association model. Our measure is based in the family of divergences introduced by Burbea and Rao [1] Burbea, J. and Rao, C. R. 1982a. On the convexity of some divergence measures based on entropy functions. IEEE Transactions on Information Theory, 28: 489–495. [Crossref], [Web of Science ®] , [Google Scholar]. Some well-known sets of data are reanalyzed and a simulation study is presented to analyze the behavior of the new families of test statistics introduced in this paper.     

A Bayesian Approach for Nonlinear Regression Models with Continuous Errors

Abstract

In this paper we develop a Bayesian analysis for the nonlinear regression model with errors that follow a continuous autoregressive process. In this way, unequally spaced observations do not present a problem in the analysis. We employ the Gibbs sampler, (see Gelfand, A., Smith, A. (1990 Gelfand, A. and Smith, A. 1990. Sampling based approaches to calculating marginal densities. J. Amer. Statist. Assoc., 85: 398–409. [Taylor & Francis Online], [Web of Science ®] , [Google Scholar]). Sampling based approaches to calculating marginal densities. J. Amer. Statist. Assoc. 85:398–409.), as the foundation for making Bayesian inferences. We illustrate these Bayesian inferences with an analysis of a real data-set. Using these same data, we contrast the Bayesian approach with a generalized least squares technique.     

Nonparametric Bivariate Estimation with Left-Truncated and Right-Censored Data

ABSTRACT

In this article we consider estimating the bivariate survival function observations where one of the components is subject to left truncation and right censoring and the other is subject to right censoring only. Two types of nonparametric estimators are proposed. One is in the form of inverse-probability-weighted average (Satten and Datta, 2001 Satten , G. A. , Datta , S. ( 2001 ). The Kaplan–Meier estimator as an inverse-probability-of-censoring weighted average . Amer. Statist. 55 : 207 – 210 . [CROSSREF] [Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) and the other is a generalization of Dabrowska's 1988 Dabrowska , D. M. ( 1988 ). Kaplan–Meier estimate on the plane . Ann. Statist. 18 : 308 – 325 . [Google Scholar] estimator. The two are then compared based on their empirical performances.     

SECOND-ORDER ASYMPTOTICS FOR SCORE TESTS IN HETEROSKEDASTIC t REGRESSION MODELS

ABSTRACT

This paper develops corrected score tests for heteroskedastic t regression models, thus generalizing results by Cordeiro, Ferrari and Paula[1] Cordeiro, G.M., Ferrari, S.L.P. and Paula, G.A. 1993. Improved Score Tests for Generalized Linear Models. Journal of the Royal Statistical Society B, 55: 661–674.  [Google Scholar] and Cribari-Neto and Ferrari[2] Cribari-Neto, F. and Ferrari, S.L.P. 1995. Second-order Asymptotics for Score Tests in Generalised Linear Models. Biometrika, 82: 426–432. [Crossref], [Web of Science ®] , [Google Scholar] for normal regression models and by Ferrari and Arellano-Valle[3] Ferrari, S.L.P. and Arellano-Valle, R. 1996. Modified Likelihood Ratio and Score Tests in Linear Regression Models Using the t Distribution. Brazilian Journal of Probability and Statistics, 10: 15–33.  [Google Scholar] for homoskedastic t regression models. We present, in matrix notation, Bartlett-type correction formulae to improve score tests in this class of models. The corrected score statistics have a chi-squared distribution to order n ^?1, where n is the sample size. We apply our main result to a few special models and present simulation results comparing the performance of the usual score tests and their corrected versions.     

Tests Concerning Equicorrelation Matrices with Grouped Normal Data

ABSTRACT

This article considers three practical hypotheses involving the equicorrelation matrix for grouped normal data. We obtain statistics and computing formulae for common test procedures such as the score test and the likelihood ratio test. In addition, statistics and computing formulae are obtained for various small sample procedures as proposed in Skovgaard (2001 Skovgaard , I. M. . ( 2001 ). Likelihood asymptotics . Scand. J. Statist. . 28 : 3 – 32 . [CROSSREF] [Crossref], [Web of Science ®] , [Google Scholar]). The properties of the tests for each of the three hypotheses are compared using Monte Carlo simulations.     

Inference Using Latent Variables for Mixtures of Distributions for Censored Data with Partial Identification

Abstract

In this article two methods are proposed to make inferences about the parameters of a finite mixture of distributions in the context of partially identifiable censored data. The first method focuses on a mixture of location and scale models and relies on an asymptotic approximation to a suitably constructed augmented likelihood; the second method provides a full Bayesian analysis of the mixture based on a Gibbs sampler. Both methods make explicit use of latent variables and provide computationally efficient procedures compared to other methods which deal directly with the likelihood of the mixture. This may be crucial if the number of components in the mixture is not small. Our proposals are illustrated on a classical example on failure times for communication devices first studied by Mendenhall and Hader (Mendenhall, W., Hader, R. J. (1958 Mendenhall, W. and Hader, R. J. 1958. Estimation of parameters of mixed exponentially distributed failure time distributions from censored life test data. Biometrika, 45: 504–520. [Crossref], [Web of Science ®] , [Google Scholar]). Estimation of parameters of mixed exponentially distributed failure time distributions from censored life test data. Biometrika 45:504–520.). In addition, we study the coverage of the confidence intervals obtained from each of the methods by means of a small simulation exercise.     

Uniqueness of the Maximum Likelihood Estimate of the Weibull Distribution Tampered Failure Rate Model

Abstract

Bhattacharyya and Soejoeti (Bhattacharyya, G. K., Soejoeti, Z. A. (1989 Bhattacharyya, G. K. and Soejoeti, Z. A. 1989. Tampered failure rate model for step-stress accelerated life test. Commun. Statist.—Theory Meth., 18(5): 1627–1643. [Taylor & Francis Online], [Web of Science ®] , [Google Scholar]). Tampered failure rate model for step-stress accelerated life test. Commun. Statist.—Theory Meth. 18(5):1627–1643.) pro- posed the TFR model for step-stress accelerated life tests. Under the TFR model, this article proves that the maximum likelihood estimate of the shape parameters is unique for the Weibull distribution in a multiple step-stress accelerated life test, and investigates the accuracy of the maximum likelihood estimate using the Monte-Carlo simulation.     

BIAS-CORRECTED CONFIDENCE INTERVALS FOR WILDLIFE ABUNDANCE ESTIMATION

ABSTRACT

We consider the issue of bias correction when the kernel method is used in constructing confidence intervals for wildlife abundance based on transect data. Our method is based on some linear model which is the limit of the weak convergence of the kernel estimate process (after suitable centering and scaling) (See Bhattacharya and Mack,[21] Bhattacharya, P.K. and Mack, Y.P. 1987. Weak Convergence of k-NN Density and Regression Estimators with Varying k and Applications. Annals of Statistics, 15: 976–994.  [Google Scholar] also Mack and Müller[22] Mack, Y.P. and Müller, H.-G. 1987. Adaptive Nonparametric Estimation of a Multivariate Regression Function. J. Mult. Analysis, 23: 169–182. [Crossref], [Web of Science ®] , [Google Scholar]). The implementation of this method is demonstrated on a well-known example in transect sampling, alongside with two other bias-reduction devices: one based on the jackknife and the other one involving the estimation of the second derivative term in the Taylor expansion of the asymptotic bias. Some comments are made in comparison with the Fourier method.     

A Similarity Measure Based on Species Proportions

ABSTRACT

There are several indices for measuring the similarity of two populations, including the ratio of the number of shared species to the number of distinct species (Jaccard's index) and the conditional probability of observing a shared species (Smith et al., 1996 Smith , W. , Solow , A. R. , Preston , P. E. ( 1996 ). An estimator of species overlap using a modified beta-binomial model. Biometrics 52 : 1472 – 1477 . [CSA] [CROSSREF] [Crossref], [Web of Science ®] , [Google Scholar]). However, these indices only take into account the number of species and species proportions of shared species. In this article, we propose a new similarity index which includes the species proportions of both the shared and non shared species in each population, and also propose a Nonparametric Maximum Likelihood Estimator (NPMLE) for this index. Bootstrap and delta methods are used to evaluate the standard errors of the NPMLE. Based on a loss function, we also compare a class of nonparametric estimators for the proposed index in various situations.     

EVALUATION OF POWER OF TESTS INVOLVING COVARIATES UNDER NONCONSTANT VARIANCE

In many experiments where pre-treatment and post-treatment measurements are taken, investigators wish to determine if there is a difference between two treatment groups. For this type of data, the post-treatment variable is used as the primary comparison variable and the pre-treatment variable is used as a covariate. Although most of the discussion in this paper is written with the pre-treatment variable as the covariate the results are applicable to other choices of a covariate. Tests based on residuals have been proposed as alternatives to the usual covariance methods. Our objective is to investigate how the powers of these tests are affected when the conditional variance of the post-treatment variable depends on the magnitude of the pre-treatment variable. In particular, we investigate two cases. [1] Crager, Michael R. 1987. Analysis of Covariance in Parallel-Group Clinical Trials With Pretreatment Baselines. Biometrics, 43: 895–901. [Crossref], [PubMed], [Web of Science ®] , [Google Scholar] The conditional variance of the post-treatment variable gradually increases as the magnitude of the pre-treatment variable increases. (In many biological models this is the case.) [2] Knoke, James D. 1991. Nonparametric Analysis of Covariance for Comparing Change in Randomized Studies with Baseline Values Subject to Error. Biometrics, 47: 523–533. [Crossref], [PubMed], [Web of Science ®] , [Google Scholar] The conditional variance of the post-treatment variable is dependent upon natural or imposed subgroups contained within the pre-treatment variable. Power comparisons are made using Monte Carlo techniques.