Bayesian latent variable model for mixed continuous and ordinal responses with possibility of missing responses

A general framework is proposed for joint modelling of mixed correlated ordinal and continuous responses with missing values for responses, where the missing mechanism for both kinds of responses is also considered. Considering the posterior distribution of unknowns given all available information, a Markov Chain Monte Carlo sampling algorithm via winBUGS is used for estimating the posterior distribution of the parameters. For sensitivity analysis to investigate the perturbation from missing at random to not missing at random, it is shown how one can use some elements of covariance structure. These elements associate responses and their missing mechanisms. Influence of small perturbation of these elements on posterior displacement and posterior estimates is also studied. The model is illustrated using data from a foreign language achievement study.     

Checking identifiability of covariance parameters in linear mixed effects models

To build a linear mixed effects model, one needs to specify the random effects and often the associated parametrized covariance matrix structure. Inappropriate specification of the structures can result in the covariance parameters of the model not identifiable. Non-identifiability can result in extraordinary wide confidence intervals, and unreliable parameter inference. Sometimes software produces implication of model non-identifiability, but not always. In the simulation of fitting non-identifiable models we tried, about half of the times the software output did not look abnormal. We derive necessary and sufficient conditions of covariance parameters identifiability which does not require any prior model fitting. The results are easy to implement and are applicable to commonly used covariance matrix structures.     

The identification of logistic regression models with errors in the variables

The simple logistic regression model with normal measurement error and normal regressor is shown to be identifiable without any extra information about the measurement error. The multiple logistic regression model with more than one regressor variable measured with error is not identifiable. If the covariance matrix of the measurement error is known up to a scalar factor, the model is identified. Further we discuss why in spite of the identifiability the models cannot be estimated in a reasonable way without extra information about the measurement error.     

Local influence of nonlinear mixed effects model based on M-estimation

Abstract

In this work we mainly study the local influence in nonlinear mixed effects model with M-estimation. A robust method to obtain maximum likelihood estimates for parameters is presented, and the local influence of nonlinear mixed models based on robust estimation (M-estimation) by use of the curvature method is systematically discussed. The counting formulas of curvature for case weights perturbation, response variable perturbation and random error covariance perturbation are derived. Simulation studies are carried to access performance of the methods we proposed. We illustrate the diagnostics by an example presented in Davidian and Giltinan, which was analyzed under the non-robust situation.     

Semiparametric Estimation of a Two-component Mixture Model where One Component is known

Abstract.  We consider a two-component mixture model where one component distribution is known while the mixing proportion and the other component distribution are unknown. These kinds of models were first introduced in biology to study the differences in expression between genes. The various estimation methods proposed till now have all assumed that the unknown distribution belongs to a parametric family. In this paper, we show how this assumption can be relaxed. First, we note that generally the above model is not identifiable, but we show that under moment and symmetry conditions some 'almost everywhere' identifiability results can be obtained. Where such identifiability conditions are fulfilled we propose an estimation method for the unknown parameters which is shown to be strongly consistent under mild conditions. We discuss applications of our method to microarray data analysis and to the training data problem. We compare our method to the parametric approach using simulated data and, finally, we apply our method to real data from microarray experiments.     

The Covariance Inflation Criterion for Adaptive Model Selection

We propose a new criterion for model selection in prediction problems. The covariance inflation criterion adjusts the training error by the average covariance of the predictions and responses, when the prediction rule is applied to permuted versions of the data set. This criterion can be applied to general prediction problems (e.g. regression or classification) and to general prediction rules (e.g. stepwise regression, tree-based models and neural nets). As a by-product we obtain a measure of the effective number of parameters used by an adaptive procedure. We relate the covariance inflation criterion to other model selection procedures and illustrate its use in some regression and classification problems. We also revisit the conditional bootstrap approach to model selection.     

Structured measurement error in nutritional epidemiology: applications in the Pregnancy, Infection, and Nutrition (PIN) Study

Preterm birth, defined as delivery before 37 completed weeks' gestation, is a leading cause of infant morbidity and mortality. Identifying factors related to preterm delivery is an important goal of public health professionals who wish to identify etiologic pathways to target for prevention. Validation studies are often conducted in nutritional epidemiology in order to study measurement error in instruments that are generally less invasive or less expensive than "gold standard" instruments. Data from such studies are then used in adjusting estimates based on the full study sample. However, measurement error in nutritional epidemiology has recently been shown to be complicated by correlated error structures in the study-wide and validation instruments. Investigators of a study of preterm birth and dietary intake designed a validation study to assess measurement error in a food frequency questionnaire (FFQ) administered during pregnancy and with the secondary goal of assessing whether a single administration of the FFQ could be used to describe intake over the relatively short pregnancy period, in which energy intake typically increases. Here, we describe a likelihood-based method via Markov Chain Monte Carlo to estimate the regression coefficients in a generalized linear model relating preterm birth to covariates, where one of the covariates is measured with error and the multivariate measurement error model has correlated errors among contemporaneous instruments (i.e. FFQs, 24-hour recalls, and/or biomarkers). Because of constraints on the covariance parameters in our likelihood, identifiability for all the variance and covariance parameters is not guaranteed and, therefore, we derive the necessary and suficient conditions to identify the variance and covariance parameters under our measurement error model and assumptions. We investigate the sensitivity of our likelihood-based model to distributional assumptions placed on the true folate intake by employing semi-parametric Bayesian methods through the mixture of Dirichlet process priors framework. We exemplify our methods in a recent prospective cohort study of risk factors for preterm birth. We use long-term folate as our error-prone predictor of interest, the food-frequency questionnaire (FFQ) and 24-hour recall as two biased instruments, and serum folate biomarker as the unbiased instrument. We found that folate intake, as measured by the FFQ, led to a conservative estimate of the estimated odds ratio of preterm birth (0.76) when compared to the odds ratio estimate from our likelihood-based approach, which adjusts for the measurement error (0.63). We found that our parametric model led to similar conclusions to the semi-parametric Bayesian model.     

Using Auxiliary Data for Binomial Parameter Estimation with Nonignorable Nonresponse

Nonignorable nonresponse is a nonresponse mechanism that depends on the values of the variable having nonresponse. When an observed data of a binomial distribution suffer missing values from a nonignorable nonresponse mechanism, the binomial distribution parameters become unidentifiable without any other auxiliary information or assumption. To address the problems of non identifiability, existing methods mostly based on the log-linear regression model. In this article, we focus on the model when the nonresponse is nonignorable and we consider to use the auxiliary data to improve identifiability; furthermore, we derive the maximum likelihood estimator (MLE) for the binomial proportion and its associated variance. We present results for an analysis of real-life data from the SARS study in China. Finally, the simulation study shows that the proposed method gives promising results.     

Frailty Models for Arbitrarily Censored and Truncated Data

In this paper, we propose a frailty model for statistical inference in the case where we are faced with arbitrarily censored and truncated data. Our results extend those of Alioum and Commenges (1996), who developed a method of fitting a proportional hazards model to data of this kind. We discuss the identifiability of the regression coefficients involved in the model which are the parameters of interest, as well as the identifiability of the baseline cumulative hazard function of the model which plays the role of the infinite dimensional nuisance parameter. We illustrate our method with the use of simulated data as well as with a set of real data on transfusion-related AIDS.     

Influence diagnostics in a multivariate normal regression model with general parameterization

Patriota and Lemonte [24] introduced a quite general multivariate normal regression model. This model considers that the mean vector and the covariance matrix share the same vector of parameters. In this paper we present some influence assessment for this model, such as the local influence, total local influence of an individual and generalized leverage which are discussed. Additionally, the normal curvatures for local influence studies are derived under some perturbation schemes.     

Joint mean–covariance model in generalized partially linear varying coefficient models for longitudinal data

In longitudinal data analysis, efficient estimation of regression coefficients requires a correct specification of certain covariance structure, and efficient estimation of covariance matrix requires a correct specification of mean regression model. In this article, we propose a general semiparametric model for the mean and the covariance simultaneously using the modified Cholesky decomposition. A regression spline-based approach within the framework of generalized estimating equations is proposed to estimate the parameters in the mean and the covariance. Under regularity conditions, asymptotic properties of the resulting estimators are established. Extensive simulation is conducted to investigate the performance of the proposed estimator and in the end a real data set is analysed using the proposed approach.     

Linear model estimation errors with estimated design parameters

The problem of error estimation of parameters b in a linear model,Y = Xb+ e, is considered when the elements of the design matrix X are functions of an unknown ‘design’ parameter vector c. An estimated value c is substituted in X to obtain a derived design matrix [Xtilde]. Even though the usual linear model conditions are not satisfied with [Xtilde], there are situations in physical applications where the least squares solution to the parameters is used without concern for the magnitude of the resulting error. Such a solution can suffer from serious errors.

This paper examines bias and covariance errors of such estimators. Using a first-order Taylor series expansion, we derive approximations to the bias and covariance matrix of the estimated parameters. The bias approximation is a sum of two terms:One is due to the dependence between ? and Y; the other is due to the estimation errors of ? and is proportional to b, the parameter being estimated. The covariance matrix approximation, on the other hand, is composed of three omponents:One component is due to the dependence between ? and Y; the second is the covariance matrix ∑_b corresponding to the minimum variance unbiased b, as if the design parameters were known without error; and the third is an additional component due to the errors in the design parameters. It is shown that the third error component is directly proportional to bb'. Thus, estimation of large parameters with wrong design matrix [Xtilde] will have larger errors of estimation. The results are illustrated with a simple linear example.     

Local influence analysis in the growth curve model with Rao's simple covariance structure

In this paper we discuss the likelihood-based local influence in a growth curve model with Rao's simple covariance structure. Under an abstract perturbation, the Hessian matrix is provided in which the eigenvector corresponding to the maximum absolute eigenvalue is used to assess the influence of observations. Specifically, we employ covariance-weighted perturbation to demonstrate the use of the proposed approach. A practical example is analysed using the proposed local influence approach.     

The prediction distribution for the heteroscedastic multivariate lineary models

The heceroscedastic multivariate linear model with multivariate normal error distribution has been considered, using the structural relation of the model, the prediction distribution of future responses of the model has been derived. it is observed that for known covariance parameters the prediction distribution of the model has a product of m multivariate Student t distribution. It is to be noted that the prediction distribution for the Student t error also has a product of m multivariate Student t distribution. Some special cases have been discussed.     

PARAMETRIC FRACTIONAL IMPUTATION FOR NON‐IGNORABLE CATEGORICAL MISSING DATA WITH FOLLOW‐UP

Incomplete data subject to non‐ignorable non‐response are often encountered in practice and have a non‐identifiability problem. A follow‐up sample is randomly selected from the set of non‐respondents to avoid the non‐identifiability problem and get complete responses. Glynn, Laird, & Rubin analyzed non‐ignorable missing data with a follow‐up sample under a pattern mixture model. In this article, maximum likelihood estimation of parameters of the categorical missing data is considered with a follow‐up sample under a selection model. To estimate the parameters with non‐ignorable missing data, the EM algorithm with weighting, proposed by Ibrahim, is used. That is, in the E‐step, the weighted mean is calculated using the fractional weights for imputed data. Variances are estimated using the approximated jacknife method. Simulation results are presented to compare the proposed method with previously presented methods.     

The Posterior Distribution of the Parameters of Component Lifetimes Based on Autopsy Data in a Shock Model

In this paper we consider a binary, monotone system whose component states are dependent through the possible occurrence of independent common shocks, i.e. shocks that destroy several components at once. The individual failure of a component is also thought of as a shock. Such systems can be used to model common cause failures in reliability analysis. The system may be a technological one, or a human being. It is observed until it fails or dies. At this instant, the set of failed components and the failure time of the system are noted. The failure times of the components are not known. These are the so-called autopsy data of the system. For the case of independent components, i.e. no common shocks, Meilijson (1981), Nowik (1990), Antoine et al . (1993) and GTsemyr (1998) discuss the corresponding identifiability problem, i.e. whether the component life distributions can be determined from the distribution of the observed data. Assuming a model where autopsy data is known to be enough for identifia bility, Meilijson (1994) goes beyond the identifiability question and into maximum likelihood estimation of the parameters of the component lifetime distributions based on empirical autopsy data from a sample of several systems. He also considers life-monitoring of some components and conditional life-monitoring of some other. Here a corresponding Bayesian approach is presented for the shock model. Due to prior information one advantage of this approach is that the identifiability problem represents no obstacle. The motivation for introducing the shock model is that the autopsy model is of special importance when components can not be tested separately because it is difficult to reproduce the conditions prevailing in the functioning system. In Gåsemyr & Natvig (1997) we treat the Bayesian approach to life-monitoring and conditional life- monitoring of components     

Parsimonious Estimation of the Covariance Matrix in Multinomial Probit Models

This article presents a Bayesian analysis of a multinomial probit model by building on previous work that specified priors on identified parameters. The main contribution of our article is to propose a prior on the covariance matrix of the latent utilities that permits elements of the inverse of the covariance matrix to be identically zero. This allows a parsimonious representation of the covariance matrix when such parsimony exists. The methodology is applied to both simulated and real data, and its ability to obtain more efficient estimators of the covariance matrix and regression coefficients is assessed using simulated data.     

Identifiability and bias reduction in the skew-probit model for a binary response

The skew-probit link function is one of the popular choices for modelling the success probability of a binary variable with regard to covariates. This link deviates from the probit link function in terms of a flexible skewness parameter. For this flexible link, the identifiability of the parameters is investigated. Next, to reduce the bias of the maximum likelihood estimator of the skew-probit model we propose to use the penalized likelihood approach. We consider three different penalty functions, and compare them via extensive simulation studies. Based on the simulation results we make some practical recommendations. For the illustration purpose, we analyse a real dataset on heart-disease.     

Effects of the estimation of covariance matrix parameters in the generalized multivariate linear model

We Consider the generalized multivariate linear model and assume the covariance matrix of the p x 1 vector of responses on a given individual can be represented in the general linear structure form described by Anderson (1973). The effects of the use of estimates of the parameters of the covariance matrix on the generalized least squares estimator of the regression coefficients and on the prediction of a portion of a future vector, when only the first portion of the vector has been observed, are investigated. Approximations are derived for the covariance matrix of the generalized least squares estimator and for the mean square error matrix of the usual predictor, for the practical case where estimated parameters are used.     

The Identifiability of Dependent Competing Risks Models Induced by Bivariate Frailty Models

In this paper, we propose to use a special class of bivariate frailty models to study dependent censored data. The proposed models are closely linked to Archimedean copula models. We give sufficient conditions for the identifiability of this type of competing risks models. The proposed conditions are derived based on a property shared by Archimedean copula models and satisfied by several well‐known bivariate frailty models. Compared with the models studied by Heckman and Honoré and Abbring and van den Berg, our models are more restrictive but can be identified with a discrete (even finite) covariate. Under our identifiability conditions, expectation–maximization (EM) algorithm provides us with consistent estimates of the unknown parameters. Simulation studies have shown that our estimation procedure works quite well. We fit a dependent censored leukaemia data set using the Clayton copula model and end our paper with some discussions. © 2014 Board of the Foundation of the Scandinavian Journal of Statistics