The Identification of Potential Longitudinal Biomarkers and Measurements of Effectiveness for Biomarkers as Surrogates in Multivariate Survival Data

A proposed method based on frailty models is used to identify longitudinal biomarkers or surrogates for a multivariate survival. This method is an extention of earlier models by Wulfsohn and Tsiatis (1997 Wulfsohn , M. S. , Tsiatis , A. A. ( 1997 ). A joint model for survival and longitudinal data measured with error . Biometrics 53 ( 1 ): 330 – 339 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]) and Song et al. (2002 Song , X. , Davidian , M. , Tsiatis , A. A. ( 2002 ). A Semiparametric likelihood approach to joint modeling of longitudinal and time-to-event data . Biometrics 58 ( 4 ): 742 – 753 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]). In this article, similar to Henderson et al. (2002 Henderson , R. , Diggle , P. J. , Dobson , A. ( 2002 ). Identification and efficacy of longitudinal markers for survival . Biostatistics 3 ( 1 ): 33 – 50 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]), a joint likelihood function combines the likelihood functions of the longitudinal biomarkers and the multivariate survival times. We use simulations to explore how the number of individuals, the number of time points per individual and the functional form of the random effects from the longitudianl biomarkers influence the power to detect the association of a longitudinal biomarker and the multivariate survival time. The proposed method is illustrate by using the gastric cancer data.     

On Testing Sample Selection Bias Under the Multicollinearity Problem

ABSTRACT

This paper reviews and extends the literature on the finite sample behavior of tests for sample selection bias. Monte Carlo results show that, when the “multicollinearity problem” identified by Nawata (1993 Nawata , K. ( 1993 ). A note on the estimation of models with sample-selection biases . Economics Letters 42 : 15 – 24 . [CSA] [CROSSREF] [Crossref], [Web of Science ®] , [Google Scholar]) is severe, (i) the t-test based on the Heckman–Greene variance estimator can be unreliable, (ii) the Likelihood Ratio test remains powerful, and (iii) nonnormality can be interpreted as severe sample selection bias by Maximum Likelihood methods, leading to negative Wald statistics. We also confirm previous findings (Leung and Yu, 1996 Leung , S. F. , Yu , S. ( 1996 ). On the choice between sample selection and two-part models . Journal of Econometrics 72 : 197 – 229 . [CSA] [CROSSREF] [Crossref], [Web of Science ®] , [Google Scholar]) that the standard regression-based t-test (Heckman, 1979 Heckman , J. J. ( 1979 ). Sample selection bias as a specification error . Econometrica 47 : 153 – 161 . [CSA] [Crossref], [Web of Science ®] , [Google Scholar]) and the asymptotically efficient Lagrange Multiplier test (Melino, 1982 Melino , A. ( 1982 ). Testing for sample selection bias . Review of Economic Studies 49 : 151 – 153 . [CSA] [Crossref], [Web of Science ®] , [Google Scholar]), are robust to nonnormality but have very little power.     

Empirical Likelihood Ratio for Linear Transformation Models with Doubly Censored Data

Double censoring arises when T represents an outcome variable that can only be accurately measured within a certain range, [L, U], where L and U are the left- and right-censoring variables, respectively. When L is always observed, we consider the empirical likelihood inference for linear transformation models, based on the martingale-type estimating equation proposed by Chen et al. (2002 Chen , K. , Jin , Z. , Ying , Z. ( 2002 ). Semiparametric analysis of transformation models with censored data . Biometrika 89 : 659 – 668 .[Crossref], [Web of Science ®] , [Google Scholar]). It is demonstrated that both the approach of Lu and Liang (2006 Lu , W. , Liang , Y. ( 2006 ). Empirical likelihood inference for linear transformation models . Journal of Multivariate Analysis 97 : 1586 – 1599 .[Crossref], [Web of Science ®] , [Google Scholar]) and that of Yu et al. (2011 Yu , W. , Sun , Y. , Zheng , M. ( 2011 ). Empirical likelihood method for linear transformation models . Annals of the Institute of Statistical Mathematics 63 : 331 – 346 .[Crossref], [Web of Science ®] , [Google Scholar]) can be extended to doubly censored data. Simulation studies are conducted to investigate the performance of the empirical likelihood ratio methods.     

A Euclidean Likelihood Estimator for Bivariate Tail Dependence

The spectral measure plays a key role in the statistical modeling of multivariate extremes. Estimation of the spectral measure is a complex issue, given the need to obey a certain moment condition. We propose a Euclidean likelihood-based estimator for the spectral measure which is simple and explicitly defined, with its expression being free of Lagrange multipliers. Our estimator is shown to have the same limit distribution as the maximum empirical likelihood estimator of Einmahl and Segers (2009 Einmahl , J. H. J. , Segers , J. ( 2009 ). Maximum empirical likelihood estimation of the spectral measure of an extreme-value distribution . Ann. Statist. 37 ( 5B ): 2953 – 2989 .[Crossref], [Web of Science ®] , [Google Scholar]). Numerical experiments suggest an overall good performance and identical behavior to the maximum empirical likelihood estimator. We illustrate the method in an extreme temperature data analysis.     

An Extension of the Epsilon-Skew-Normal Distribution

This article is related with the probabilistic and statistical properties of an parametric extension of the so-called epsilon-skew-normal (ESN) distribution introduced by Mudholkar and Hutson (2000 Mudholkar , G. S. , Hutson , A. D. ( 2000 ). The epsilon-skew-normal distribution for analyzing near-normal data . J. Statist. Plann. Infer. 83 : 291 – 309 .[Crossref], [Web of Science ®] , [Google Scholar]), which considers an additional shape parameter in order to increase the flexibility of the ESN distribution. Also, this article concerns likelihood inference about the parameters of the new class. In particular, the information matrix of the maximum likelihood estimators is obtained, showing that it is non singular in the special normal case. Finally, the statistical methods are illustrated with two examples based on real datasets.     

The Alpha-power Tobit Model

The main object of this article is to propose an extension of the tobit model for which the error distribution follows the power-normal distribution (Gupta and Gupta, 2008 Gupta , D. , Gupta , R. C. ( 2008 ). Analyzing skewed data by power normal model . Test 17 : 197 – 210 .[Crossref], [Web of Science ®] , [Google Scholar]). Inference is dealt with by using the likelihood approach. Simulation studies and application to a real data set are used to demonstrate the usefulness of the extension.     

Bias-Corrected Maximum Likelihood Estimators in Nonlinear Heteroscedastic Models

Nonlinear heteroscedastic models are widely used in econometrics and statistical applications. We derive matrix formulae for the second-order biases of the maximum likelihood estimators of the parameters in the mean and variance response which generalize previous results by Cook et al. (1986 Cook , D. R. , Tsai , C. L. , Wei , B. C. ( 1986 ). Bias in nonlinear regression . Biometrika 73 : 615 – 623 .[Crossref], [Web of Science ®] , [Google Scholar]) and Cordeiro (1993 Cordeiro , G. M. ( 1993 ). Bartlett corrections and bias correction for two heteroscedastic regression models . Commun. Statist. Theor. Meth. 22 : 169 – 188 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]). The biases of the estimators are easily obtained as vectors of regression coefficients from suitable weighted linear regressions. The practical use of such biases is illustrated in a simulation study and in an application to a real data set.     

Covariance Matrix Formula for Exponential Family Nonlinear Models

This article gives a matrix formula for second-order covariances of maximum likelihood estimators in exponential family nonlinear models, thus generalizing the result of Cordeiro (2004 Cordeiro , G. M. ( 2004 ). Second-order covariance matrix of maximum likelihood estimates in generalized linear models . Statist. Probab. Lett. 66 : 153 – 160 .[Crossref], [Web of Science ®] , [Google Scholar]) valid for generalized linear models with known dispersion parameter. Some simulations show that the second-order covariances for exponential family nonlinear models can be quite pronounced in small to moderate sample sizes.     

Second-Order Covariance Matrix Formula for Heteroskedastic Generalized Linear Models

For the first time, we provide a matrix formula for second-order covariances of maximum likelihood estimates in heteroskedastic generalized linear models, thus generalizing the results of Cordeiro (2004 Cordeiro , G. M. ( 2004 ). Second-order covariance matrix of maximum likelihood estimates in generalized linear models . Statist. Probab. Lett. 66 : 153 – 160 .[Crossref], [Web of Science ®] , [Google Scholar]) and Cordeiro et al. (2006 Cordeiro , G. M. , Barroso , L. P. , Botter , D. A. (2006). Covariance matrix formula for generalized linear models with unknown dispersion. Commun. Statist. Theor. Meth. 35:113–120.[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) related to the generalized linear models with known and unknown dispersion parameter, respectively. The covariance matrix formula does not involve cumulants of log-likelihood derivatives and can be easily obtained using simple matrix operations. We apply our main result to a simple model. Some simulations show that the second-order covariances can be quite pronounced in small to moderate samples. The usual covariances of the maximum likelihood estimates can be corrected by these second-order covariances.     

Tests for Multiple Outliers in an Exponential Sample

By applying the recursion of Huffer (1988 Huffer, F. 1988. Divided differences and the joint distribution of linear combinations of spacings. Journal of Applied Probability, 25: 346–354. [Crossref], [Web of Science ®] , [Google Scholar]) repeatedly, we propose an algorithm for evaluating the null joint distribution of Dixon-type test statistics for testing discordancy of k upper outliers in exponential samples. By using the critical values of Dixon-type test statistics determined from the proposed algorithm and those of Cochran-type test statistics presented earlier by Lin and Balakrishnan (2009 Lin, C. T. and Balakrishnan, N. 2009. Exact computation of the null distribution of a test for multiple outliers in an exponential sample. Computational Statistics & Data Analysis, 53: 3281–3290. [Crossref], [Web of Science ®] , [Google Scholar]), we carry out an extensive Monte Carlo study to investigate the powers and the error probabilities for the effects of masking and swamping when the number of outliers k = 2 and 3. Based on our empirical findings, we recommend Rosner’s (1975 Rosner, B. 1975. On the detection of many outliers. Technometrics, 17: 221–227. [Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) sequential test procedure based on Dixon-type test statistics for testing multiple outliers from an exponential distribution.     

DSGE Models with Student-t Errors

This paper deals with Dynamic Stochastic General Equilibrium (DSGE) models under a multivariate student-t distribution for the structural shocks. Based on the solution algorithm of Klein (2000) and the gamma-normal representation of the t-distribution, the TaRB-MH algorithm of Chib and Ramamurthy (2010 Chib , S. , Ramamurthy , S. ( 2010 ). Tailored randomized block MCMC methods with application to DSGE models . Journal of Econometrics 108 : 19 – 38 .[Crossref], [Web of Science ®] , [Google Scholar]) is used to estimate the model. A technique for estimating the marginal likelihood of the DSGE student-t model is also provided. The methodologies are illustrated first with simulated data and then with the DSGE model of Ireland (2004 Ireland , P. N. ( 2004 ). Technology shocks in the new keynesian model . Review of Economics and Statistics 86 ( 4 ): 923 – 936 .[Crossref], [Web of Science ®] , [Google Scholar]) where the results support the t-error model in relation to the Gaussian model.     

Factor Stochastic Volatility in Mean Models: A GMM Approach

This paper provides a semiparametric framework for modeling multivariate conditional heteroskedasticity. We put forward latent stochastic volatility (SV) factors as capturing the commonality in the joint conditional variance matrix of asset returns. This approach is in line with common features as studied by Engle and Kozicki (1993 Engle , R. F. , Kozicki , S. ( 1993 ). Testing for common features . Journal of Business and Economic Statistics 11 ( 4 ): 369 – 395 . [CSA] [CROSSREF] [Taylor & Francis Online], [Web of Science ®] , [Google Scholar]), and it allows us to focus on identication of factors and factor loadings through first- and second-order conditional moments only. We assume that the time-varying part of risk premiums is based on constant prices of factor risks, and we consider a factor SV in mean model. Additional specification of both expectations and volatility of future volatility of factors provides conditional moment restrictions, through which the parameters of the model are all identied. These conditional moment restrictions pave the way for instrumental variables estimation and GMM inference.     

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.     

General Saddlepoint Approximations: Application to the Anderson-Darling Test Statistic

We consider the relative merits of various saddlepoint approximations for the cumulative distribution function (cdf) of a statistic with a possibly non normal limit distribution. In addition to the usual Lugannani-Rice approximation, we also consider approximations based on higher-order expansions, including the case where the base distribution for the approximation is taken to be non normal. This extends earlier work by Wood et al. (1993 Wood , A. T. A. , Booth , J. G. , Butler , R. W. ( 1993 ). Saddlepoint approximations to the CDF of some statistics with nonnormal limit distributions . Journal of the American Statistical Association 88 : 680 – 686 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]). These approximations are applied to the distribution of the Anderson-Darling test statistic. While these generalizations perform well in the middle of the distribution's support, a conventional normal-based Lugannani-Rice approximation (Giles, 2001 Giles , D. E. A. ( 2001 ). A Saddlepoint approximation to the distribution function of the Anderson-Darling test statistic . Communications in Statistics B 30 : 899 – 905 .[Taylor & Francis Online] , [Google Scholar]) is superior for conventional critical regions.     

Bayesian Capture-Recapture Analysis: An Application in Modeling Semelparity of a Neotropical Didelphid Marsupial

We develop a series of Bayesian statistical models for estimating survival of a neotropic didelphid marsupial, the Brazilian gracile mouse opossum (Gracilinanus microtarsus). These models are based on the Cormack–Jolly–Seber model (Cormack, 1964 Cormack , R. M. ( 1964 ). Estimates of survival from the sighting of marked animals . Biometrika 51 : 429 – 438 .[Crossref], [Web of Science ®] , [Google Scholar]; Jolly 1965 Jolly , G. M. ( 1965 ). Explicit estimates from capture-recapture data with both death and immigration stochastic model . Biometrika 52 : 225 – 247 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]; Seber 1965 Seber , G. A. F. ( 1965 ). A note on the multiple recapture census . Biometrika 52 : 249 – 259 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]) with both survival and recapture rates expressed as a function of covariates using a logit link. The proposed models allow taking into account heterogeneity in capture probability caused by the existence of different groups of individuals in the population. The models were applied to two cohorts (Cohort, 2000, 2001) with the first one including 14 and the second one 15 sampling occasions. The best models for each of the cohorts indicate that G. microtarsus is best described as partially semelparous, a condition in which mortality after the first mating is high but graded over time, with a fraction of males surviving for a second breeding season (Boonstra, 2005 Boonstra , R. ( 2005 ). Equipped for life: the adaptive role of the stress axis in male mammals . Journal of Mammalogy 86 : 236 – 247 .[Crossref], [Web of Science ®] , [Google Scholar]).     

Deriving Approximations in a Random Effects Model for Multicenter Clinical Trials with Binary Response

The design and analysis of multicenter trials based on a random effects model is well developed for a continuous response, but is less well developed for a binary response. Here we describe a random effects model for a binary response for two treatments and show how maximum likelihood estimates for the unknown treatment difference can be derived using a novel approximation to the likelihood. The suggested approximation is easy to use and seems to be better suited to the problem than the Laplace approximation and the approximation based on adaptive Gaussian quadratures. We also derive an approximation for the Fisher information matrix of the treatment parameters. The results extend those previously reviewed by Agresti and Hartzel (2000 Agresti , A. , Hartzel , J. ( 2000 ). Strategies for comparing treatments on a binary response with multi-centre data . Statist. Med. 19 : 1115 – 1139 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]).     

Estimators for the Population Mean in the Case of Missing Data

We propose a class of estimators for the population mean when there are missing data in the data set. Obtaining the mean square error equations of the proposed estimators, we show the conditions where the proposed estimators are more efficient than the sample mean, ratio-type estimators, and the estimators in Singh and Horn (2000 Singh , S. , Horn , S. ( 2000 ). Compromised imputation in survey sampling . Metrika 51 : 267 – 276 .[Crossref], [Web of Science ®] , [Google Scholar]) and Singh and Deo (2003 Singh , S. , Deo , B. (2003). Imputation by power transformation. Statist. Pap. 44:555–579.[Crossref], [Web of Science ®] , [Google Scholar]) in the case of missing data. These conditions are also supported by a numerical example.     

On Rates of Convergence for Posterior Distributions Under Misspecification

We extend the approach of Walker (2003 Walker , S. ( 2003 ). On sufficient conditions for Bayesian consistency . Biometrika 90 ( 2 ): 482 – 488 .[Crossref], [Web of Science ®] , [Google Scholar]); (2004 Walker , S. ( 2004 ). New approaches to Bayesian consistency . Ann. Statist. 32 ( 5 ): 2028 – 2043 .[Crossref], [Web of Science ®] , [Google Scholar]) to the case of misspecified models. A sufficient condition for establishing rates of convergence is given based on a key identity involving martingales, which does not require construction of tests. We also show roughly that the result obtained by using tests can also be obtained by our approach, which demonstrates the potential wider applicability of this method.     

A Multivariate Threshold Varying Conditional Correlations Model

In this article, a multivariate threshold varying conditional correlation (TVCC) model is proposed. The model extends the idea of Engle (2002 Engle , R. F. ( 2002 ). Dynamic conditional correlation: a simple class of multivariate generalized autoregressive conditional heteroskedasticity models . Journal of Business and Economic Statistics 20 ( 3 ): 339 – 350 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) and Tse and Tsui (2002 Tse , Y. K. , Tsui , A. K. C. ( 2002 ). A multivariate GARCH model with time-varying correlations . Journal of Business and Economic Statistics , July 2002 , 20 ( 3 ): 351 – 362 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) to a threshold framework. This model retains the interpretation of the univariate threshold GARCH model and allows for dynamic conditional correlations. Techniques of model identification, estimation, and model checking are developed. Some simulation results are reported on the finite sample distribution of the maximum likelihood estimate of the TVCC model. Real examples demonstrate the asymmetric behavior of the mean and the variance in financial time series and the ability of the TVCC model to capture these phenomena.     

Second-Order Powers of a Class of Tests in the Presence of a Nuisance Parameter

The second-order local powers of a broad class of asymptotic chi-squared tests are considered in a composite case where both the parameter of interest and the nuisance parameter are possibly multidimensional for which no assumption has been made regarding global parametric orthogonality or curved exponentiality. The main result is that the second-order (point-by-point) local power identity holds if approximate third cumulants of a square-root version of the (modified) test statistic in the class vanish up to the second-order, which is an extension of Kakizawa (2010a Kakizawa , Y. ( 2010a ). Second-order power comparison of tests . Commun. Statist. Theor. Meth. 39 : 1424 – 1436 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) in the absence of the nuisance parameter. It is also shown that in the presence of the nuisance parameter, such a third cumulant condition does not always imply the second-order local unbiasedness of the resulting test. Then, the adjusted likelihood ratio test by Mukerjee (1993b Mukerjee , R. ( 1993b ). An extension of the conditional likelihood ratio test to the general multiparameter case . Ann. Inst. Statist. Math. 45 : 759 – 771 .[Crossref], [Web of Science ®] , [Google Scholar]) can be interpreted as the second-order local unbiased modification after applying the third cumulant condition.