Estimation of Survivorship Function Based on Doubly Censored Data with Application to HIV/AIDS

Left censoring concept has been defined in different ways in statistical applications. Turnbull (1974 Turnbull , B. W. ( 1974 ). Nonparametric estimation of a survivorship function with doubly censored data . J. Amer. Statist. Assoc. 69 : 169 – 173 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) defines it in a particular way. Whereas in recent literature, especially in epidemiological studies, it has been defined in another way. This difference between the two approaches is the main reason that despite simplicity, Turnbull method cannot be applicable in all cases of doubly censored data. In this article we present a modified Turnbull method for analysis of doubly censored data adequate with recent definition. Comparison has been done with other statistical methods, including imputation estimator, full likelihood-based and conditional likelihood-based approach using Iranian HIV data.     

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.     

SCAD-Penalized Least Absolute Deviation Regression in High-Dimensional Models

When outliers and/or heavy-tailed errors exist in linear models, the least absolute deviation (LAD) regression is a robust alternative to the ordinary least squares regression. Existing variable-selection methods in linear models based on LAD regression either only consider the finite number of predictors or lack the oracle property associated with the estimator. In this article, we focus on the variable selection via LAD regression with a diverging number of parameters. The rate of convergence of the LAD estimator with the smoothly clipped absolute deviation (SCAD) penalty function is established. Furthermore, we demonstrate that, under certain regularity conditions, the penalized estimator with a properly selected tuning parameter enjoys the oracle property. In addition, the rank correlation screening method originally proposed by Li et al. (2011 Li, G.R., Peng, H., Zhu, L.X. (2011). Nonconcave penalized M-estimation with a diverging number of parameters. Statistica Sinica 21:391–419.[Web of Science ®] , [Google Scholar]) is applied to deal with ultrahigh dimensional data. Simulation studies are conducted for revealing the finite sample performance of the estimator. We further illustrate the proposed methodology by a real example.     

On Simultaneous Estimation of the Number of Signals and Frequencies of Multiple Sinusoids When Some Observations Are Missing

In an earlier article (Bai et al., 1999 Bai , Z. D. , Rao , C. R. , Wu , Y. H. , Zen , M. M. , Zhao , L. C. ( 1999 ). The simultaneous estimation of the number of signals and frequencies of multiple sinusods when some observations are missing: I. Asymptotics . Proc. Natl. Acad. Sci. 96 : 11,106 – 11,110 . [CSA] [Crossref], [Web of Science ®] , [Google Scholar]), the problem of simultaneous estimation of the number of signals and frequencies of multiple sinusoids is considered in the case that some observations are missing. The number of signals is estimated with an information theoretic criterion and the frequencies are estimated with eigenvariation linear prediction. Asymptotic properties of the procedure are investigated but the Monte Carlo simulation is not performed. In this article, a slightly different but scale invariant criterion for detection is proposed and the estimation of frequencies remains the same. Asymptotic properties of this new procedure are provided. Monte Carlo Simulation for both procedures is carried out. Furthermore, comparison on the real signals is also given.     

Tuning Parameter Estimation in Penalized Least Squares Methodology

The efficiency of the penalized methods (Fan and Li, 2001 Fan , J. , Li , R. ( 2001 ). Variable selection via nonconcave penalized likelihood and its oracle properties . Journal of the American Statistical Association 96 : 1348 – 1360 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) depends strongly on a tuning parameter due to the fact that it controls the extent of penalization. Therefore, it is important to select it appropriately. In general, tuning parameters are chosen by data-driven approaches, such as the commonly used generalized cross validation. In this article, we propose an alternative method for the derivation of the tuning parameter selector in penalized least squares framework, which can lead to an ameliorated estimate. Simulation studies are presented to support theoretical findings and a comparison of the Type I and Type II error rates, considering the L ₁, the hard thresholding and the Smoothly Clipped Absolute Deviation penalty functions, is performed. The results are given in tables and discussion follows.     

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.     

Estimation of the covariance matrix with two-step monotone missing data

Abstract

We suggest shrinkage based technique for estimating covariance matrix in the high-dimensional normal model with missing data. Our approach is based on the monotone missing scheme assumption, meaning that missing values patterns occur completely at random. Our asymptotic framework allows the dimensionality p grow to infinity together with the sample size, N, and extends the methodology of Ledoit and Wolf (2004) Ledoit, O., Wolf, M. (2004). A well-conditioned estimator for large dimensional covariance matrices. J. Multivariate Anal. 88:365–411.[Crossref], [Web of Science ®] , [Google Scholar] to the case of two-step monotone missing data. Two new shrinkage-type estimators are derived and their dominance properties over the Ledoit and Wolf (2004) Ledoit, O., Wolf, M. (2004). A well-conditioned estimator for large dimensional covariance matrices. J. Multivariate Anal. 88:365–411.[Crossref], [Web of Science ®] , [Google Scholar] estimator are shown under the expected quadratic loss. We perform a simulation study and conclude that the proposed estimators are successful for a range of missing data scenarios.     

Multilevel Augmented Pairs Second-Order Response Surface Designs and Their Robustness to Missing Data

Missing observations can occur even in a well-planned experiment. The effect of missing observations can be much more serious when the design is saturated or near saturated. The levels of factor settings that make a design more robust to missing observations are of great importance in the sense that the loss for missing observations becomes minimum. In this study, new augmented pairs minimax loss designs are constructed, which are more robust to one missing design point than the augmented pairs designs presented by Morris (2000 Morris , M. D. ( 2000 ). A class of three-level experimental designs for response surface modeling . Technometrics 42 : 111 – 121 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]). New designs are compared with augmented pairs designs, central composite designs, and small composite designs under generalized scaled standard deviations. The model used is also studied for the regression coefficient estimates.     

Regression Analysis with Covariates Missing at Random: A Piece-wise Nonparametric Model for Missing Covariates

Statistical analysis for the regression model f _β(y | x, z) with missing values in the covariate vector X requires modeling of the covariate distribution g(x | z). Likelihood methods, including Ibrahim (1990 Ibrahim , J. G. ( 1990 ). Incomplete data in generalized linear models . J. Amer. Statist. Assoc. 85 : 765 – 769 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]), Chen (2004 Chen , H. Y. (2004). Nonparametric and semiparametric models for missing covariates in parametric regression. J. Amer. Statist. Assoc. 99:1176–1189.[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]), and Zhao (2005 Zhao , Y. ( 2005 ). Design and Efficient Estimation in Regression Analysis with Missing Data in Two-Phase Studies. Ph.D. thesis , University of Waterloo . [Google Scholar]), need either X or Z to be discrete. This article considers extending the likelihood methods to deal with cases where both X and Z may be continuous. We propose modeling the covariate distribution g(x | z) using a piece-wise nonparametric model, then a maximum likelihood estimate (MLE) of β can be computed following the maximum likelihood estimating procedure of Chen (2004 Chen , H. Y. (2004). Nonparametric and semiparametric models for missing covariates in parametric regression. J. Amer. Statist. Assoc. 99:1176–1189.[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) or Zhao (2005 Zhao , Y. ( 2005 ). Design and Efficient Estimation in Regression Analysis with Missing Data in Two-Phase Studies. Ph.D. thesis , University of Waterloo . [Google Scholar]). The resulting estimation method is easy to implement and the asymptotic properties of the MLE follow under certain conditions. Extensive simulation studies for different models indicate that the proposed method is acceptable for practical implementation. A real data example is used to illustrate the method.     

A Bayesian Meta-Modeling Approach for Gaussian Stochastic Process Models Using a Non Informative Prior

In this article, an efficient Bayesian meta-modeling approach is proposed for Gaussian stochastic process models in computer experiments. Different prior densities and particularly, a non informative hyper prior have been employed on the parameters involved in the correlation matrix. And the estimation of related parameters is obtained by the expectation-maximization algorithm. Compared with the recent work of Li and Sudjianto (2005 Li , R. , Sudjianto , A. ( 2005 ). Analysis of computer experiments using penalized likelihood in Kriging models . Technometrics 47 : 111 – 120 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]), the proposed approach is not only of higher prediction accuracy but also of lower computational cost, due to the utilization of the non informative prior and the absence of tuning parameters. Experimental results demonstrate that our approach yields state-of-the-art performance.     

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.     

Group Variable Selection with Oracle Property by Weight-Fused Adaptive Elastic Net Model for Strongly Correlated Data

This paper is the generalization of weight-fused elastic net (Fu and Xu, 2012 Fu, G., Xu, Q. (2012). Grouping variable selection by weight fused elastic net for multi-collinear data. Communications in Statistics-Simulation and Computation 41(2):205–221.[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]), which performs group variable selection by combining weight-fused LASSO(wfLasso) and elastic net (Zou and Hastie, 2005 Zou, H., Hastie, T. (2005). Regularization and variable selection via the elastic net. Journal of the Royal Statistical Society: Series B (Statistical Methodology) 67(2):301–320.[Crossref], [Web of Science ®] , [Google Scholar]) penalties. In this study, the elastic net penalty is replaced by adaptive elastic net penalty (AdaEnet) (Zou and Zhang, 2009 Zou, H., Zhang, H. (2009). On the adaptive elastic-net with a diverging number of parameters. Annals of Statistics 37(4):1733–1751.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]), and a new group variable selection algorithm with oracle property (Fan and Li, 2001 Fan, J., Li, R. (2001). Variable selection via nonconcave penalized likelihood and its oracle properties. Journal of the American Statistical Association 96(456):1348–1360.[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]; Zou, 2006 Zou, H. (2006). The adaptive lasso and its oracle properties. Journal of the American Statistical Association 101(476):1418–1429.[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) is obtained.     

An Asymmetric Kernel Estimator of Density Function for Stationary Associated Sequences

Here, we apply the smoothing technique proposed by Chaubey et al. (2007 Chaubey , Y. P. , Sen , A. , Sen , P. K. ( 2007 ). A new smooth density estimator for non-negative random variables. Technical Report No. 1/07. Department of Mathematics and Statistics, Concordia University, Montreal, Canada . [Google Scholar]) for the empirical survival function studied in Bagai and Prakasa Rao (1991 Bagai , I. , Prakasa Rao , B. L. S. ( 1991 ). Estimation of the survival function for stationary associated processes . Statist. Probab. Lett. 12 : 385 – 391 .[Crossref], [Web of Science ®] , [Google Scholar]) for a sequence of stationary non-negative associated random variables.The derivative of this estimator in turn is used to propose a nonparametric density estimator. The asymptotic properties of the resulting estimators are studied and contrasted with some other competing estimators. A simulation study is carried out comparing the recent estimator based on the Poisson weights (Chaubey et al., 2011 Chaubey , Y. P. , Dewan , I. , Li , J. ( 2011 ). Smooth estimation of survival and density functions for a stationary associated process using poisson weights . Statist. Probab. Lett. 81 : 267 – 276 .[Crossref], [Web of Science ®] , [Google Scholar]) showing that the two estimators have comparable finite sample global as well as local behavior.     

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.     

Improved Predictive Inference for Responses Based on Location Parameter Median from the Rayleigh Model Given a Doubly Censored Sample

The purpose of this article is to investigate the predictive inference for responses from the location parameter mean as well as from the median given a doubly censored sample from the two-parameter Rayleigh model. The predictive results by Khan et al. (2010 Khan , H. M. R. , Provost , S. B. , Ashima , S. ( 2010 ). Predictive Inference from a Two-Parameter Rayleigh Life Model Given a Doubly Censored Sample . Commun. Statist. Theor. Meth. 39 ( 7 ): 1237 – 1246 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) are used to obtain the predictive inference for responses from the median, where Khan et al. (2010 Khan , H. M. R. , Provost , S. B. , Ashima , S. ( 2010 ). Predictive Inference from a Two-Parameter Rayleigh Life Model Given a Doubly Censored Sample . Commun. Statist. Theor. Meth. 39 ( 7 ): 1237 – 1246 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) obtained the future estimates from the mean. A numerical example representing 66 liver cancer patients is used for predictive analysis. It is concluded that the predictive inference from the median gives precise results as compared with the location parameter mean.     

Maximum Likelihood Estimation in Compound Geometric Failure Model with Changing Parameters From Type-I Two-Stage Progressively Censored and Group Censored Samples

Boardman and Kendell (1970 Boardman , T. J. , Kendell , P. J. ( 1970 ). Estimation in compound failure models . Technometrics 12 : 891 – 908 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) considered the problem of estimation with respect to Type-I censoring when an item is subjected to only one of the two causes of failure assuming exponential model. Patel and Gajjar (1992 Patel , M. N. , Gajjar , A. V. ( 1992 ). Maximum likelihood estimation in compound exponential failure model with changing failure rates from Type-I progressively censored and group censored samples . Commun. Statist. Theor. Meth. 21 ( 10 ): 2899 – 2908 .[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) considered extension of the Boardman and Kendell's results in case of two-stage progressive censoring. Here we have considered geometric competing risk failure model with two independent causes of failures. Maximum likelihood estimation of the parameters is carried out using Type-I two-stage progressively censored and group censored samples. Asymptotic standard errors of the estimators are obtained for both the cases. Two illustrative examples are cited for ungroup and group competing risk models.     

Combined estimating function for random coefficient models with correlated errors

ABSTRACT

Estimating functionshave been shown to be convenient to study inference for non linear time series models. Recently, Thavaneswaran et al. (2012 Thavaneswaran, A., Liang, Y., Frank, J. (2012). Inference for random coefficient volatility models. Stat. Probab. Lett. 82(12):2086–2090.[Crossref], [Web of Science ®] , [Google Scholar]) used combined estimating functions to study inference for random coefficient autoregressive (RCA) models with generalized autoregressive heteroscedasticity errors. While most RCA modeling assumes that the random term and the error are independent, Chandra and Taniguchi (2001 Chandra, S.A., Taniguchi, M. (2001). Estimating functions for nonlinear time series models. Ann. Inst. Stat. Math 53(1):125–141.[Crossref], [Web of Science ®] , [Google Scholar]) studied inference for RCA models with correlated errors using linear estimating functions. In this paper, we derive the quadratic estimating functions for the joint estimation of the conditional mean, variance, and correlation parameters of the RCA models with correlated errors.     

Estimating Incidence Rate on Current Status Data with Application to a Phase IV Cancer Trial

New drug discovery in the pediatrics has dramatically improved survival, but with long- term adverse events. This motivates the examination of adverse outcomes such as long-term toxicity in a phase IV trial. An ideal approach to monitor long-term toxicity is to systematically follow the survivors, which is generally not feasible. Instead, cross-sectional surveys are conducted in Hudson et al. (2007 Hudson , M. M. , Rai , S. N. , Nunez , C. , Merchant , T. E. , Marina , N. M. , Zalamea , N. , Cox , C. , Phipps , S. , Pompeu , R. , Rosenthal , D. ( 2007 ). Noninvasive evaluation of late anthracycline cardiac toxicity in childhood cancer survivors . J. Clin. Oncol. 25 : 3635 – 3643 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]), with one of the objectives to estimate the cumulative incidence rates along with specific interest in fixed-term (5 or 10 year) rates. We present inference procedures based on current status data to our motivating example with very interesting findings.     

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.     

Optimality of ratio type estimation methods for population mean in the presence of missing data

This article proposes various Searls-type ratio imputation methods (STRIM) on the lines of Ahmed et al. (2006 Ahmed, M. S., O. Al-Titi, Z. Al-Rawi, and W. Abu-Dayyeh. 2006. Estimation of a population mean using different imputation methods. Stat. Trans. 7 (6):1247–1264. [Google Scholar]). It is a well-known fact that the optimal ratio type estimator attains the MSE of regression estimator (or optimal difference estimator) but while using Searls-type transformation (STT) (Searls (1964 Searls, D. T. 1964. The utilization of a known coefficient of variation in the estimation procedure. J. Am. Stat. Assoc. 59:1225–1226.[Taylor &; Francis Online], [Web of Science ®] , [Google Scholar])) this may not always happen. These STRIM are shown to perform better than the imputation procedures of Ahmed et al. (2006 Ahmed, M. S., O. Al-Titi, Z. Al-Rawi, and W. Abu-Dayyeh. 2006. Estimation of a population mean using different imputation methods. Stat. Trans. 7 (6):1247–1264. [Google Scholar]). The STRIM may even outperform the Searls type difference imputation methods (STDIM) proposed by us in our earlier work, Bhushan and Pandey (2016 Bhushan, S., and A. P. Pandey. 2016. Optimal imputation of the missing data for estimation of population mean. Journal of Statistics and Management System 19 (6):755–69.[Taylor &; Francis Online], [Web of Science ®] , [Google Scholar]). This study is concluded with the numerical study along with the theoretical comparison.