Testing economic “genetic pleiotropy” for Box-Cox linear model

Abstract

Genetic pleiotropy occurs when a single gene influences two or more seemingly unrelated phenotypic traits. It is significant to detect pleiotropy and understand its causes. However, most current statistical methods to discover pleiotropy mainly test the null hypothesis that none of the traits is associated with a variant, which departures from the null to test just one associated trait or k associated traits. Schaid et al. (2016 Schaid, D. J., X. Tong, B. Larrabee, R. B. Kennedy, G. A. Poland, and J. P. Sinnwell. 2016. Statistical methods for testing genetic pleiotropy. Genetics 204 (2):483–97. doi:10.1534/genetics.116.189308.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]) first proposed a sequential testing framework to analyze pleiotropy based on a linear model and a multivariate normal distribution. In this paper, we analyze the Economic pleiotropy which occurs when an economic action or policy influences two or more economic phenomena. In this paper, we extend the linear model to Box-Cox transformation model and proposed a new decision method. It improves the efficiency of hypothesis test and controls the Type I error. We then apply the method using economic data to multivariate sectoral employments in response to governmental expenditures and provide a quantitative assessment and some insights of different impacts from economic policy.     

Optimal nonparametric estimator of the area under ROC curve based on clustered data

Abstract

In diagnostic trials, clustered data are obtained when several subunits of the same patient are observed. Intracluster correlations need to be taken into account when analyzing such clustered data. A nonparametric method has been proposed by Obuchowski (1997 Obuchowski, N. A. 1997. Nonparametric analysis of clustered ROC curve data. Biometrics 53 (2):567–78.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]) to estimate the Receiver Operating Characteristic curve area (AUC) for such clustered data. However, Obuchowski’s estimator is not efficient as it gives equal weight to all pairwise rankings within and between cluster. In this paper, we propose a more efficient nonparametric AUC estimator with two sets of optimal weights. Simulation results show that the loss of efficiency of Obuchowski’s estimator for a single AUC or the AUC difference can be substantial when there is a moderate intracluster test correlation and the cluster size is large. The efficiency gain of our weighted AUC estimator for a single AUC or the AUC difference is further illustrated using the data from a study of screening tests for neonatal hearing.     

Survival analysis for a new compounded bivariate failure time distribution in shock and competing risk models via an EM algorithm

Abstract

In this paper, two bivariate models based on the proposed methods of Marshall and Olkin are introduced. In the first model, the new bivariate distribution is presented based on the proposed method of Marshall and Olkin (1967 Marshall, A. W., and I. Olkin. 1967. A multivariate exponential distribution. Journal of the American Statistical Association 62 (317):30–44. doi: 10.2307/2282907.[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) which has natural interpretations, and it can be applied in fatal shock models or in competing risks models. In the second model, the proposed method of Marshall and Olkin (1997 Marshall, A. W., and I. Olkin. 1997. A new method of adding a parameter to a family of distributions with application to the exponential and weibull families. Biometrika 84 (3):641–52. doi: 10.1093/biomet/84.3.641.[Crossref], [Web of Science ®] , [Google Scholar]) is generalized to bivariate case and a new bivariate distribution is introduced. We call these new distributions as the bivariate Gompertz (BGP) distribution and bivariate Gompertz-geometric (BGPG) distribution, respectively. Moreover, the BGP model can be obtained as a special case of the BGPG model. Then, we present various properties of the new bivariate models. In this regard, the joint and conditional density functions, the joint cumulative distribution function can be obtained in compact forms. Also, the aging properties and the bivariate hazard gradient are discussed. This model has five unknown parameters and the maximum likelihood estimators cannot be obtained in explicit form. We propose to use the EM algorithm to compute the maximum likelihood estimators of the unknown parameters, and it is computationally quite tractable. Also, Monte Carlo simulations are performed to investigate the effectiveness of the proposed algorithm. Finally, we analyze three real data sets for illustrative purposes.     

On a class exhibiting trend change in average failure rate

Abstract

Weak convergence and moment convergence issues are investigated for the New Better than Average Failure Rate (NBAFR) family (introduced by Loh (1984 Loh, W. Y. 1984. A new generalization of the class of NBU distributions. IEEE Transactions on Reliability R-33 :97–113[Crossref], [Web of Science ®] , [Google Scholar])). We explore the validity of these results in the context of a more general ageing class that we introduce. We prove some new properties of this class and derive its interrelationships with other non-monotonic ageing families. Reliability and moment bounds are obtained and an interesting characterization of exponentiality is proved. Special cases of our results lead to new theorems for the NBAFR class. Finally weak convergence and related issues are established for this class.     

The Johnson System of Frequency Curves—Historical,Graphical, and Limiting Perspectives

Abstract

The idea of transforming one random variate to another with a more convenient density has been developed in the first half of the 20th century. In his thesis, Norman L. Johnson (1917–2004) developed a pioneering system of transformations of the standard normal distribution which gained substantial popularity in the second half of the 20th century and beyond. In Johnson’s 1949 Johnson, N. L. (1949), “Systems of Frequency Curves Generated by Methods of Translation,” Biometrika, 36, 149–176.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar] Biometrika paper entitled Systems of frequency curves generated by methods of translation, summarizing that thesis, one of his primary interests was the behavior of the shape of the probability density functions as their parameter values change. Herein, we attempt to further elucidate this behavior through a series of geometric expositions of that transformation process. In these expositions insight is obtained into the behavior of Johnson’s density functions, and their skewness and kurtosis, as they converge to their limiting distributions, a topic which received little attention.     

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.     

A nonparametric specification test for the volatility functions of diffusion processes

This paper develops a new test for the parametric volatility function of a diffusion model based on nonparametric estimation techniques. The proposed test imposes no restriction on the functional form of the drift function and has an asymptotically standard normal distribution under the null hypothesis of correct specification. It is consistent against any fixed alternatives and has nontrivial asymptotic power against a class of local alternatives with proper rates. Monte Carlo simulations show that the test performs well in finite samples and generally has better power performance than the nonparametric test of Li (2007 Li, F. (2007). Testing the parametric specification of the diffusion function in a diffusion process. Econometric Theory 23(2):221–250.[Crossref], [Web of Science ®] , [Google Scholar]) and the stochastic process-based tests of Dette and Podolskij (2008 Dette, H., Podolskij, M. (2008). Testing the parametric form of the volatility in continuous time diffusion models–a stochastic process approach. Journal of Econometrics 143(1):56–73.[Crossref], [Web of Science ®] , [Google Scholar]). When applying the test to high frequency data of EUR/USD exchange rate, the empirical results show that the commonly used volatility functions fit more poorly when the data frequency becomes higher, and the general volatility functions fit relatively better than the constant volatility function.     

The exponential distribution analog of the Grubbs–Weaver method

Abstract

Grubbs and Weaver (1947 Grubbs, F. E., and C. L. Weaver. 1947. The best unbiased estimate of population standard deviation based on group ranges. Journal of the American Statistical Association 42 (238):224–41. doi: 10.2307/2280652.[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) suggest a minimum-variance unbiased estimator for the population standard deviation of a normal random variable, where a random sample is drawn and a weighted sum of the ranges of subsamples is calculated. The optimal choice involves using as many subsamples of size eight as possible. They verified their results numerically for samples of size up to 100, and conjectured that their “rule of eights” is valid for all sample sizes. Here we examine the analogous problem where the underlying distribution is exponential and find that a “rule of fours” yields optimality and prove the result rigorously.     

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]).     

An Inverse-Probability-Weighted Approach to the Estimation of Successive Duration Times under Left-Truncation and Right-Censoring

In incident cohort studies, survival data often include subjects who have had an initiate event at recruitment and may potentially experience two successive events (first and second) during the follow-up period. Since the second duration process becomes observable only if the first event has occurred, left-truncation and dependent censoring arise if the two duration times are correlated. To confront the two potential sampling biases, Chang and Tzeng (2006 Chang , S.-H. , Tzeng , S.-J. (2006). Noparametric estimation of sojourn time distributions for truncated serial event data- a weight-adjusted approach. Lifetime Data Anal. 53–67.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]) provided an inverse-probability-weighted (IPW) approach for estimating the joint probability function of successive duration times. In this note, an alternative IPW approach is proposed. A simulation study is conducted to compare the two IPW approaches.     

Complete integral convergence for arrays of row-wise extended independent random variables under Sub-linear expectations

Abstract

In this paper, we establish the complete convergence and complete integral convergence for arrays of row-wise extended independent random variables under sub-linear expectation space with some conditions. At the same time we extend some complete convergence and complete integral convergence theorems from the classical probability space to the sub-linear expectation space. The results generalize corresponding results obtained by Wu et al. (2017 Zhang, L. X. 2016b. Exponential inequalities under the sub-linear expectations with applications to laws of the iterated logarithm. Science China Mathematics 59 (12):2503–26. doi: 10.1007/s11425-016-0079-1.[Crossref], [Web of Science ®] , [Google Scholar]).     

Tests of Multivariate Independence for Ordinal Data

Population and sample versions of Kendall and Spearman measures of association suitable for multivariate ordinal data are defined. The latter generalize the indices of dependence of Ruymgaart and van Zuijlen (1978 Ruymgaart , F. H. , van Zuijlen , M. C. A. ( 1978 ). Asymptotic normality of multivariate linear rank statistics in the non-i.i.d. case . Ann. Statist. 6 : 588 – 602 .[Crossref], [Web of Science ®] , [Google Scholar]), Joe (1990 Joe , H. ( 1990 ). Multivariate concordance . J. Multivariate Anal. 35 : 12 – 30 .[Crossref], [Web of Science ®] , [Google Scholar]), and Schmid and Schmidt (2007 Schmid , F. , Schmidt , R. ( 2007 ). Multivariate extensions of Spearman's rho and related statistics . Statist. Probab. Lett. 77 : 407 – 416 .[Crossref], [Web of Science ®] , [Google Scholar]) by allowing atoms in the underlying distribution. The representation of the proposed empirical measures as U-statistics enables to establish their asymptotic normality under general distributions. A special attention is given to tests of independence for multivariate ordinal data, where the power of the new methodologies are investigated under fixed and contiguous alternatives.     

A Broad Class of Partially Specified Autoregressions on Multi-Casting Data

Extending the bifurcating autoregressive (BAR) process (cf. Cowan and Staudte, 1986 Cowan , R. , Staudte , R. G. ( 1986 ). The bifurcating autoregression model in cell lineage studies . Biometrics 42 : 769 – 783 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]) to multi-casting (multi-splitting) data, Hwang and Choi (2009 Hwang , S. Y. , Choi , M. S. ( 2009 ). Modeling and large sample estimation for multi-casting autoregression . Statist. Prob. Lett. 79 : 1943 – 1950 .[Crossref], [Web of Science ®] , [Google Scholar]) introduced multi-casting autoregression (MCAR, for short) defined on multi-casting tree structured data. This article is concerned with the case when the MCAR model is partially specified only through conditional mean and variance without directly imposing autoregressive (AR) structure. The resulting class of models will be referred to as P-MCAR (partially specified MCAR). The P-MCAR considerably enlarges the class of multi-casting models including (as special cases) MCAR, random coefficient MCAR, conditionally heteroscedastic multi-casting models and binomial-thinning processes. Moment structures for this broad P-MCAR class are investigated. Least squares (LS) estimation method is discussed and asymptotic relative efficiency (ARE) of the generalized-LS over ordinary-LS is obtained in a closed form. A simulation study is conducted to illustrate results.     

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.     

Use of scrambled response for estimating mean of the sensitivity variable

Abstract

In this article, we propose new efficient and more generalized difference-cum-exponential type estimator and generalized-difference-cum-generalized exponential type estimators for estimating the mean of sensitivity variable using the auxiliary information. We also discuss theoretically that proposed generalized estimators are more efficient than Sousa et al. (2010 Sousa, R., J. Shabbir, P. C. Real, and S. Gupta. 2010. Ratio estimation of the mean of a sensitive variable in the presence of auxiliary information. Journal of Statistical Theory and Practice 4 (3):495–507.[Taylor & Francis Online] , [Google Scholar]), Gupta et al. (2012 Gupta, S., J. Shabbir, R. Sousa, and P. C. Real. 2012. Estimation of the mean of a sensitive variable in the presence of auxiliary information. Communications in Statistics-Theory and Methods 41:1–12.[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) and Koyuncu, Gupta, and Sousa (2014 Koyuncu, N., S. Gupta, and R. Sousa. 2014. Exponential-type estimators of the mean of a sensitive variable in the presence of non sensitive auxiliary information. Communications in Statistics-Simulation and Computation 43 (7):1583–94. doi: 10.1080/03610918.2012.737492.[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) estimators. Results from a real life application and simulation study are presented to demonstrate the performance of the proposed mean estimators in relation to some of the existing mean estimators.     

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.     

Hazards Regression for Cancer Studies

The complication in analyzing tumor data is that the tumors detected in a screening program tend to be slowly progressive tumors, which is the so-called length-biased sampling that is inherent in screening studies. Under the assumption that all subjects have the same tumor growth function, Ghosh (2008 Ghosh , D. ( 2008 ). Proportional hazards regression for cancer studies . Biometrics 64 : 141 – 148 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]) developed estimation procedures for proportional hazards model. In this article, by modeling growth function as a function of covariates, we demonstrate that Ghosh (2008 Ghosh , D. ( 2008 ). Proportional hazards regression for cancer studies . Biometrics 64 : 141 – 148 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar])'s approach can be extended to the case when each subject has a specific growth function. A simulation study is conducted to demonstrate the potential usefulness of the proposed estimators for the regression parameters in the proportional and additive hazards model.     

Variance estimation in adaptive cluster sampling

Abstract

In this paper, a class of variance estimator is proposed of a finite population variance under an adaptive cluster sampling design in the presence of information on an auxiliary variable. We obtain expressions for the mean square error and bias for the developed estimators and their performance is evaluated on a Poisson clustered process and a real data set. The simulation study evaluates the efficiency of the suggested estimators for an adaptive cluster sampling (ACS) design and the Isaki (1983 Isaki, C. T. 1983. Variance estimation using auxiliary information. Journal of the American Statistical Association 78 (381):117–23. doi: 10.1080/01621459.1983.10477939.[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) estimator of the variance for SRSWOR over the sample variance for SRSWOR.     

Additive Mixed Effect Model for Clustered Doubly Censored Data

Cai and Zeng (2011 Cai, J. and Zeng, D. 2011. Additive mixed effect model for clustered failure time data. Biometrics, 67(4): 1340–1351. [Crossref], [PubMed] , [Google Scholar]) proposed an additive mixed effect model to analyze clustered right-censored data. In this article, we demonstrate that the approach of Cai and Zeng (2011 Cai, J. and Zeng, D. 2011. Additive mixed effect model for clustered failure time data. Biometrics, 67(4): 1340–1351. [Crossref], [PubMed] , [Google Scholar]) can be extended to clustered doubly censored data. Furthermore, when both left- and right-censoring variables are always observed, we propose alternative estimators using the approach of Cai and Cheng (2004 Cai, T. and Cheng, S. C. 2004. Semiparametric regression analysis for doubly censored data. Biometrika, 91: 277–290. [Crossref], [Web of Science ®] , [Google Scholar]). A simulation study is conducted to investigate the performance of the proposed estimators.