Detecting covariates with non-random missing values in a survey of primary education in Madagascar

A major survey of the determinants of access to primary education in Madagascar was carried out in 1994. The probability of enrolment, probability of admission, delay before beginning school, probability of repeating a year and probability of dropping out were studied. The results of the survey are briefly described. In the analysis, one major problem was non-random missing values in the covariates. Some simple methods were developed for detecting whether a response variable depends on the missingness of a given covariate and whether eliminating the missing values would distort the resulting model. A way of incorporating covariates with randomly missing values was used such that the individuals having the missing values did not need to be eliminated. These methods are described and examples are given on how they were applied for one of the key covariates that had a large number of non-random missing values and for one for which the values appear to be randomly missing.     

Estimation in a model for a semi-Markov process with covariates under right-censoring

A semi-Markov model with covariates is proposed for a multi-state process with a finite number of states such that the transition probabilities between the states and the distribution functions of the duration times between the occurrence of two states depend on a discrete covariate. The hazard rates for the time elapsed between two successive states depend on the covariate through a proportional hazards model involving a set of regression parameters, while the transition probabilities depend on the covariate in an unspecified way. We propose estimators for these parameters and for the cumulative hazard functions of the sojourn times. A difficulty comes from the fact that when a sojourn time in a state is right-censored, the next state is unknown. We prove that our estimators are consistent and asymptotically Gaussian under the model constraints.     

Influence Function Based Variance Estimation and Missing Data Issues in Case-Cohort Studies

Recognizing that the efficiency in relative risk estimation for the Cox proportional hazards model is largely constrained by the total number of cases, Prentice (1986) proposed the case-cohort design in which covariates are measured on all cases and on a random sample of the cohort. Subsequent to Prentice, other methods of estimation and sampling have been proposed for these designs. We formalize an approach to variance estimation suggested by Barlow (1994), and derive a robust variance estimator based on the influence function. We consider the applicability of the variance estimator to all the proposed case-cohort estimators, and derive the influence function when known sampling probabilities in the estimators are replaced by observed sampling fractions. We discuss the modifications required when cases are missing covariate information. The missingness may occur by chance, and be completely at random; or may occur as part of the sampling design, and depend upon other observed covariates. We provide an adaptation of S-plus code that allows estimating influence function variances in the presence of such missing covariates. Using examples from our current case-cohort studies on esophageal and gastric cancer, we illustrate how our results our useful in solving design and analytic issues that arise in practice.     

Boosting flexible functional regression models with a high number of functional historical effects

We propose a general framework for regression models with functional response containing a potentially large number of flexible effects of functional and scalar covariates. Special emphasis is put on historical functional effects, where functional response and functional covariate are observed over the same interval and the response is only influenced by covariate values up to the current grid point. Historical functional effects are mostly used when functional response and covariate are observed on a common time interval, as they account for chronology. Our formulation allows for flexible integration limits including, e.g., lead or lag times. The functional responses can be observed on irregular curve-specific grids. Additionally, we introduce different parameterizations for historical effects and discuss identifiability issues.The models are estimated by a component-wise gradient boosting algorithm which is suitable for models with a potentially high number of covariate effects, even more than observations, and inherently does model selection. By minimizing corresponding loss functions, different features of the conditional response distribution can be modeled, including generalized and quantile regression models as special cases. The methods are implemented in the open-source R package FDboost. The methodological developments are motivated by biotechnological data on Escherichia coli fermentations, but cover a much broader model class.     

Weighted-bootstrap alignment of explanatory variables

Adjustment for covariates is a time-honored tool in statistical analysis and is often implemented by including the covariates that one intends to adjust as additional predictors in a model. This adjustment often does not work well when the underlying model is misspecified. We consider here the situation where we compare a response between two groups. This response may depend on a covariate for which the distribution differs between the two groups one intends to compare. This creates the potential that observed differences are due to differences in covariate levels rather than “genuine” population differences that cannot be explained by covariate differences. We propose a bootstrap-based adjustment method. Bootstrap weights are constructed with the aim of aligning bootstrap–weighted empirical distributions of the covariate between the two groups. Generally, the proposed weighted-bootstrap algorithm can be used to align or match the values of an explanatory variable as closely as desired to those of a given target distribution. We illustrate the proposed bootstrap adjustment method in simulations and in the analysis of data on the fecundity of historical cohorts of French-Canadian women.     

Gompertz model with time-dependent covariate in the presence of interval-, right- and left-censored data

In this paper, the Gompertz model is extended to incorporate time-dependent covariates in the presence of interval-, right-, left-censored and uncensored data. Then, its performance at different sample sizes, study periods and attendance probabilities are studied. Following that, the model is compared to a fixed covariate model. Finally, two confidence interval estimation methods, Wald and likelihood ratio (LR), are explored and conclusions are drawn based on the results of the coverage probability study. The results indicate that bias, standard error and root mean square error values of the parameter estimates decrease with the increase in study period, attendance probability and sample size. Also, LR was found to work slightly better than the Wald for parameters of the model.     

The use of auxiliary variables in capture-recapture modelling: An overview

I review the use of auxiliary variables in capture-recapture models for estimation of demographic parameters (e.g. capture probability, population size, survival probability, and recruitment, emigration and immigration numbers). I focus on what has been done in current research and what still needs to be done. Typically in the literature, covariate modelling has made capture and survival probabilities functions of covariates, but there are good reasons also to make other parameters functions of covariates as well. The types of covariates considered include environmental covariates that may vary by occasion but are constant over animals, and individual animal covariates that are usually assumed constant over time. I also discuss the difficulties of using time-dependent individual animal covariates and some possible solutions. Covariates are usually assumed to be measured without error, and that may not be realistic. For closed populations, one approach to modelling heterogeneity in capture probabilities uses observable individual covariates and is thus related to the primary purpose of this paper. The now standard Huggins-Alho approach conditions on the captured animals and then uses a generalized Horvitz-Thompson estimator to estimate population size. This approach has the advantage of simplicity in that one does not have to specify a distribution for the covariates, and the disadvantage is that it does not use the full likelihood to estimate population size. Alternately one could specify a distribution for the covariates and implement a full likelihood approach to inference to estimate the capture function, the covariate probability distribution, and the population size. The general Jolly-Seber open model enables one to estimate capture probability, population sizes, survival rates, and birth numbers. Much of the focus on modelling covariates in program MARK has been for survival and capture probability in the Cormack-Jolly-Seber model and its generalizations (including tag-return models). These models condition on the number of animals marked and released. A related, but distinct, topic is radio telemetry survival modelling that typically uses a modified Kaplan-Meier method and Cox proportional hazards model for auxiliary variables. Recently there has been an emphasis on integration of recruitment in the likelihood, and research on how to implement covariate modelling for recruitment and perhaps population size is needed. The combined open and closed 'robust' design model can also benefit from covariate modelling and some important options have already been implemented into MARK. Many models are usually fitted to one data set. This has necessitated development of model selection criteria based on the AIC (Akaike Information Criteria) and the alternative of averaging over reasonable models. The special problems of estimating over-dispersion when covariates are included in the model and then adjusting for over-dispersion in model selection could benefit from further research.     

A semiparametric pseudo-score method for analysis of two-phase studies with continuous phase-I covariates

Two-phase study designs can reduce cost and other practical burdens associated with large scale epidemiologic studies by limiting ascertainment of expensive covariates to a smaller but informative sub-sample (phase-II) of the main study (phase-I). During the analysis of such studies, however, subjects who are selected at phase-I but not at phase-II, remain informative as they may have partial covariate information. A variety of semi-parametric methods now exist for incorporating such data from phase-I subjects when the covariate information can be summarized into a finite number of strata. In this article, we consider extending the pseudo-score approach proposed by Chatterjee et al. (J Am Stat Assoc 98:158–168, 2003) using a kernel smoothing approach to incorporate information on continuous phase-I covariates. Practical issues and algorithms for implementing the methods using existing software are discussed. A sandwich-type variance estimator based on the influence function representation of the pseudo-score function is proposed. Finite sample performance of the methods are studies using simulated data. Advantage of the proposed smoothing approach over alternative methods that use discretized phase-I covariate information is illustrated using two-phase data simulated within the National Wilms Tumor Study (NWTS).     

The use of auxiliary variables in capture-recapture modelling: an overview

I review the use of auxiliary variables in capture-recapture models for estimation of demographic parameters (e.g. capture probability, population size, survival probability, and recruitment, emigration and immigration numbers). I focus on what has been done in current research and what still needs to be done. Typically in the literature, covariate modelling has made capture and survival probabilities functions of covariates, but there are good reasons also to make other parameters functions of covariates as well. The types of covariates considered include environmental covariates that may vary by occasion but are constant over animals, and individual animal covariates that are usually assumed constant over time. I also discuss the difficulties of using time-dependent individual animal covariates and some possible solutions. Covariates are usually assumed to be measured without error, and that may not be realistic. For closed populations, one approach to modelling heterogeneity in capture probabilities uses observable individual covariates and is thus related to the primary purpose of this paper. The now standard Huggins-Alho approach conditions on the captured animals and then uses a generalized Horvitz-Thompson estimator to estimate population size. This approach has the advantage of simplicity in that one does not have to specify a distribution for the covariates, and the disadvantage is that it does not use the full likelihood to estimate population size. Alternately one could specify a distribution for the covariates and implement a full likelihood approach to inference to estimate the capture function, the covariate probability distribution, and the population size. The general Jolly-Seber open model enables one to estimate capture probability, population sizes, survival rates, and birth numbers. Much of the focus on modelling covariates in program MARK has been for survival and capture probability in the Cormack-Jolly-Seber model and its generalizations (including tag-return models). These models condition on the number of animals marked and released. A related, but distinct, topic is radio telemetry survival modelling that typically uses a modified Kaplan-Meier method and Cox proportional hazards model for auxiliary variables. Recently there has been an emphasis on integration of recruitment in the likelihood, and research on how to implement covariate modelling for recruitment and perhaps population size is needed. The combined open and closed 'robust' design model can also benefit from covariate modelling and some important options have already been implemented into MARK. Many models are usually fitted to one data set. This has necessitated development of model selection criteria based on the AIC (Akaike Information Criteria) and the alternative of averaging over reasonable models. The special problems of estimating over-dispersion when covariates are included in the model and then adjusting for over-dispersion in model selection could benefit from further research.     

Bayeslan Credit Ratings

In this contribution we aim at improving ordinal variable selection in the context of causal models for credit risk estimation. In this regard, we propose an approach that provides a formal inferential tool to compare the explanatory power of each covariate and, therefore, to select an effective model for classification purposes. Our proposed model is Bayesian nonparametric thus keeps the amount of model specification to a minimum. We consider the case in which information from the covariates is at the ordinal level. A noticeable instance of this regards the situation in which ordinal variables result from rankings of companies that are to be evaluated according to different macro and micro economic aspects, leading to ordinal covariates that correspond to various ratings, that entail different magnitudes of the probability of default. For each given covariate, we suggest to partition the statistical units in as many groups as the number of observed levels of the covariate. We then assume individual defaults to be homogeneous within each group and heterogeneous across groups. Our aim is to compare and, therefore select, the partition structures resulting from the consideration of different explanatory covariates. The metric we choose for variable comparison is the calculation of the posterior probability of each partition. The application of our proposal to a European credit risk database shows that it performs well, leading to a coherent and clear method for variable averaging of the estimated default probabilities.     

A Comparison of Analysis of Covariate-Adjusted Residuals and Analysis of Covariance

Various methods to control the influence of a covariate on a response variable are compared. These methods are ANOVA with or without homogeneity of variances (HOV) of errors and Kruskal–Wallis (K–W) tests on (covariate-adjusted) residuals and analysis of covariance (ANCOVA). Covariate-adjusted residuals are obtained from the overall regression line fit to the entire data set ignoring the treatment levels or factors. It is demonstrated that the methods on covariate-adjusted residuals are only appropriate when the regression lines are parallel and covariate means are equal for all treatments. Empirical size and power performance of the methods are compared by extensive Monte Carlo simulations. We manipulated the conditions such as assumptions of normality and HOV, sample size, and clustering of the covariates. The parametric methods on residuals and ANCOVA exhibited similar size and power when error terms have symmetric distributions with variances having the same functional form for each treatment, and covariates have uniform distributions within the same interval for each treatment. In such cases, parametric tests have higher power compared to the K–W test on residuals. When error terms have asymmetric distributions or have variances that are heterogeneous with different functional forms for each treatment, the tests are liberal with K–W test having higher power than others. The methods on covariate-adjusted residuals are severely affected by the clustering of the covariates relative to the treatment factors when covariate means are very different for treatments. For data clusters, ANCOVA method exhibits the appropriate level. However, such a clustering might suggest dependence between the covariates and the treatment factors, so makes ANCOVA less reliable as well.     

Better experimental design by hybridizing binary matching with imbalance optimization

We present a new experimental design procedure that divides a set of experimental units into two groups in order to minimize error in estimating a treatment effect. One concern is the elimination of large covariate imbalance between the two groups before the experiment begins. Another concern is robustness of the design to misspecification in response models. We address both concerns in our proposed design: we first place subjects into pairs using optimal nonbipartite matching, making our estimator robust to complicated nonlinear response models. Our innovation is to keep the matched pairs extant, take differences of the covariate values within each matched pair, and then use the greedy switching heuristic of Krieger et al. (2019) or rerandomization on these differences. This latter step greatly reduces covariate imbalance. Furthermore, our resultant designs are shown to be nearly as random as matching, which is robust to unobserved covariates. When compared to previous designs, our approach exhibits significant improvement in the mean squared error of the treatment effect estimator when the response model is nonlinear and performs at least as well when the response model is linear. Our design procedure can be found as a method in the open source R package available on CRAN called GreedyExperimentalDesign .     

Balanced covariates with response adaptive randomization

Response adaptive randomization (RAR) methods for clinical trials are susceptible to imbalance in the distribution of influential covariates across treatment arms. This can make the interpretation of trial results difficult, because observed differences between treatment groups may be a function of the covariates and not necessarily because of the treatments themselves. We propose a method for balancing the distribution of covariate strata across treatment arms within RAR. The method uses odds ratios to modify global RAR probabilities to obtain stratum‐specific modified RAR probabilities. We provide illustrative examples and a simple simulation study to demonstrate the effectiveness of the strategy for maintaining covariate balance. The proposed method is straightforward to implement and applicable to any type of RAR method or outcome.     

ESTIMATING THE NUMBER OF VISITS TO THE DOCTOR

The frequency of doctor consultations has direct consequences for health care budgets, yet little statistical analysis of the determinants of doctor visits has been reported. We consider the distribution of the number of visits to the doctor and, in particular, we model its dependence on a number of demographic factors. Examination of the Australian 1995 National Health Survey data reveals that generalized linear Poisson or negative binomial models are inadequate for modelling the mean as a function of covariates, because of excessive zero counts, and a mean‐variance relationship that varies enormously over covariate values. A negative binomial model is used, with parameter values estimated in subgroups according to the discrete combinations of the covariate values. Smoothing splines are then used to smooth and interpolate the parameter values. In effect the mean and the shape parameters are each modelled as (different) functions of gender, age and geographical factors. The estimated regressions for the mean have simple and intuitive interpretations. However, the dependence of the (negative binomial) shape parameter on the covariates is more difficult to interpret and is subject to influence by extreme observations. We illustrate the use of the model by estimating the distribution of the number of doctor consultations in the Statistical Local Area of Ryde, based on population numbers from the 1996 census.     

Estimation and tests for a longitudinal regression model based on the Markov chain

In this paper, the dependence of transition probabilities on covariates and a test procedure for covariate dependent Markov models are examined. The nonparametric test for the role of waiting time proposed by Jones and Crowley [M. Jones, J. Crowley, Nonparametric tests of the Markov model for survival data Biometrika 79 (3) (1992) 513–522] has been extended here to transitions and reverse transitions. The limitation of the Jones and Crowley method is that it does not take account of other covariates that might have association with the probabilities of transition. A simple test procedure is proposed that can be employed for testing: (i) the significance of association between covariates and transition probabilities, and (ii) the impact of waiting time on the transition probabilities. The procedure is illustrated using panel data on hospitalization of the elderly population in the USA from the Health and Retirement Survey (HRS).     

Information borrowing methods for covariate‐adjusted ROC curve

In medical diagnostic testing problems, the covariate adjusted receiver operating characteristic (ROC) curves have been discussed recently for achieving the best separation between disease and control. Due to various restrictions such as cost, the availability of patients, and ethical issues quite frequently only limited information is available. As a result, we are unlikely to have a large enough overall sample size to support reliable direct estimations of ROCs for all the underlying covariates of interest. For example, some genetic factors are less commonly observable compared with others. To get an accurate covariate adjusted ROC estimation, novel statistical methods are needed to effectively utilize the limited information. Therefore, it is desirable to use indirect estimates that borrow strength by employing values of the variables of interest from neighbouring covariates. In this paper we discuss two semiparametric exponential tilting models, where the density functions from different covariate levels share a common baseline density, and the parameters in the exponential tilting component reflect the difference among the covariates. With the proposed models, the estimated covariate adjusted ROC is much smoother and more efficient than the nonparametric counterpart without borrowing information from neighbouring covariates. A simulation study and a real data application are reported. The Canadian Journal of Statistics 40: 569–587; 2012 © 2012 Statistical Society of Canada     

A comparison of two approaches for power and sample size calculations in logistic regression models

Whittemore (1981) proposed an approach for calculating the sample size needed to test hypotheses with specified significance and power against a given alternative for logistic regression with small response probability. Based on the distribution of covariate, which could be either discrete or continuous, this approach first provides a simple closed-form approximation to the asymptotic covariance matrix of the maximum likelihood estimates, and then uses it to calculate the sample size needed to test a hypothesis about the parameter. Self et al. (1992) described a general approach for power and sample size calculations within the framework of generalized linear models, which include logistic regression as a special case. Their approach is based on an approximation to the distribution of the likelihood ratio statistic. Unlike the Whittemore approach, their approach is not limited to situations of small response probability. However, it is restricted to models with a finite number of covariate configurations. This study compares these two approaches to see how accurate they would be for the calculations of power and sample size in logistic regression models with various response probabilities and covariate distributions. The results indicate that the Whittemore approach has a slight advantage in achieving the nominal power only for one case with small response probability. It is outperformed for all other cases with larger response probabilities. In general, the approach proposed in Self et al. (1992) is recommended for all values of the response probability. However, its extension for logistic regression models with an infinite number of covariate configurations involves an arbitrary decision for categorization and leads to a discrete approximation. As shown in this paper, the examined discrete approximations appear to be sufficiently accurate for practical purpose.     

A Bayesian mixture of experts approach to covariate misclassification

This article considers misclassification of categorical covariates in the context of regression analysis; if unaccounted for, such errors usually result in mis-estimation of model parameters. With the presence of additional covariates, we exploit the fact that explicitly modelling non-differential misclassification with respect to the response leads to a mixture regression representation. Under the framework of mixture of experts, we enable the reclassification probabilities to vary with other covariates, a situation commonly caused by misclassification that is differential on certain covariates and/or by dependence between the misclassified and additional covariates. Using Bayesian inference, the mixture approach combines learning from data with external information on the magnitude of errors when it is available. In addition to proving the theoretical identifiability of the mixture of experts approach, we study the amount of efficiency loss resulting from covariate misclassification and the usefulness of external information in mitigating such loss. The method is applied to adjust for misclassification on self-reported cocaine use in the Longitudinal Studies of HIV-Associated Lung Infections and Complications.     

Parameter estimation in regression for long-term survival rate from censored data

In recent years, regression models have been shown to be useful for predicting the long-term survival probabilities of patients in clinical trials. The importance of a regression model is that once the regression parameters are estimated information about the regressed quantity is immediate. A simple estimator is proposed for the regression parameters in a model for the long-term survival rate. The proposed estimator is seen to arise from an estimating function that has the missing information principle underlying its construction. When the covariate takes values in a finite set, the proposed estimating function is equivalent to an ad hoc estimating function proposed in the literature. However, in general, the two estimating functions lead to different estimators of the regression parameter. For discrete covariates, the asymptotic covariance matrix of the proposed estimator is simple to calculate using standard techniques involving the predictable covariation process of martingale transforms. An ad hoc extension to the case of a one-dimensional continuous covariate is proposed. Simplicity and generalizability are two attractive features of the proposed approach. The last mentioned feature is not enjoyed by the other estimator.     

Bayesian Methods for Missing Covariates in Cure Rate Models

We propose methods for Bayesian inference for missing covariate data with a novel class of semi-parametric survival models with a cure fraction. We allow the missing covariates to be either categorical or continuous and specify a parametric distribution for the covariates that is written as a sequence of one dimensional conditional distributions. We assume that the missing covariates are missing at random (MAR) throughout. We propose an informative class of joint prior distributions for the regression coefficients and the parameters arising from the covariate distributions. The proposed class of priors are shown to be useful in recovering information on the missing covariates especially in situations where the missing data fraction is large. Properties of the proposed prior and resulting posterior distributions are examined. Also, model checking techniques are proposed for sensitivity analyses and for checking the goodness of fit of a particular model. Specifically, we extend the Conditional Predictive Ordinate (CPO) statistic to assess goodness of fit in the presence of missing covariate data. Computational techniques using the Gibbs sampler are implemented. A real data set involving a melanoma cancer clinical trial is examined to demonstrate the methodology.