Multiple imputation for competing risks regression with interval-censored data

ABSTRACT

We present here an extension of Pan's multiple imputation approach to Cox regression in the setting of interval-censored competing risks data. The idea is to convert interval-censored data into multiple sets of complete or right-censored data and to use partial likelihood methods to analyse them. The process is iterated, and at each step, the coefficient of interest, its variance–covariance matrix, and the baseline cumulative incidence function are updated from multiple posterior estimates derived from the Fine and Gray sub-distribution hazards regression given augmented data. Through simulation of patients at risks of failure from two causes, and following a prescheduled programme allowing for informative interval-censoring mechanisms, we show that the proposed method results in more accurate coefficient estimates as compared to the simple imputation approach. We have implemented the method in the MIICD R package, available on the CRAN website.     

Augmented inverse probability weighted fractional imputation in quantile regression

By employing all the observed information and the optimal augmentation term, we propose an augmented inverse probability weighted fractional imputation method (AFI) to handle covariates missing at random in quantile regression. Compared with the existing completely case analysis, inverse probability weighting, multiple imputation and fractional imputation based on quantile regression model with missing covarites, we carry out simulation study to investigate its performance in estimation accuracy and efficiency, computational efficiency and estimation robustness. We also talk about the influence of imputation replicates in our AFI. Finally, we apply our methodology to part of the National Health and Nutrition Examination Survey data.     

Multiple imputation for continuous variables using a Bayesian principal component analysis

ABSTRACT

We propose a multiple imputation method based on principal component analysis (PCA) to deal with incomplete continuous data. To reflect the uncertainty of the parameters from one imputation to the next, we use a Bayesian treatment of the PCA model. Using a simulation study and real data sets, the method is compared to two classical approaches: multiple imputation based on joint modelling and on fully conditional modelling. Contrary to the others, the proposed method can be easily used on data sets where the number of individuals is less than the number of variables and when the variables are highly correlated. In addition, it provides unbiased point estimates of quantities of interest, such as an expectation, a regression coefficient or a correlation coefficient, with a smaller mean squared error. Furthermore, the widths of the confidence intervals built for the quantities of interest are often smaller whilst ensuring a valid coverage.     

A new multivariate imputation method based on Bayesian networks

Dealing with incomplete data is a pervasive problem in statistical surveys. Bayesian networks have been recently used in missing data imputation. In this research, we propose a new methodology for the multivariate imputation of missing data using discrete Bayesian networks and conditional Gaussian Bayesian networks. Results from imputing missing values in coronary artery disease data set and milk composition data set as well as a simulation study from cancer-neapolitan network are presented to demonstrate and compare the performance of three Bayesian network-based imputation methods with those of multivariate imputation by chained equations (MICE) and the classical hot-deck imputation method. To assess the effect of the structure learning algorithm on the performance of the Bayesian network-based methods, two methods called Peter-Clark algorithm and greedy search-and-score have been applied. Bayesian network-based methods are: first, the method introduced by Di Zio et al. [Bayesian networks for imputation, J. R. Stat. Soc. Ser. A 167 (2004), 309–322] in which, each missing item of a variable is imputed using the information given in the parents of that variable; second, the method of Di Zio et al. [Multivariate techniques for imputation based on Bayesian networks, Neural Netw. World 15 (2005), 303–310] which uses the information in the Markov blanket set of the variable to be imputed and finally, our new proposed method which applies the whole available knowledge of all variables of interest, consisting the Markov blanket and so the parent set, to impute a missing item. Results indicate the high quality of our new proposed method especially in the presence of high missingness percentages and more connected networks. Also the new method have shown to be more efficient than the MICE method for small sample sizes with high missing rates.     

Efficient Robust Estimation for Linear Models with Missing Response at Random

Coefficient estimation in linear regression models with missing data is routinely carried out in the mean regression framework. However, the mean regression theory breaks down if the error variance is infinite. In addition, correct specification of the likelihood function for existing imputation approach is often challenging in practice, especially for skewed data. In this paper, we develop a novel composite quantile regression and a weighted quantile average estimation procedure for parameter estimation in linear regression models when some responses are missing at random. Instead of imputing the missing response by randomly drawing from its conditional distribution, we propose to impute both missing and observed responses by their estimated conditional quantiles given the observed data and to use the parametrically estimated propensity scores to weigh check functions that define a regression parameter. Both estimation procedures are resistant to heavy‐tailed errors or outliers in the response and can achieve nice robustness and efficiency. Moreover, we propose adaptive penalization methods to simultaneously select significant variables and estimate unknown parameters. Asymptotic properties of the proposed estimators are carefully investigated. An efficient algorithm is developed for fast implementation of the proposed methodologies. We also discuss a model selection criterion, which is based on an IC_Q ‐type statistic, to select the penalty parameters. The performance of the proposed methods is illustrated via simulated and real data sets.     

Imputation techniques for incomplete data in quadratic discriminant analysis

We have compared the efficacy of five imputation algorithms readily available in SAS for the quadratic discriminant function. Here, we have generated several different parametric-configuration training data with missing data, including monotone missing-at-random observations, and used a Monte Carlo simulation to examine the expected probabilities of misclassification for the two-class quadratic statistical discrimination problem under five different imputation methods. Specifically, we have compared the efficacy of the complete observation-only method and the mean substitution, regression, predictive mean matching, propensity score, and Markov Chain Monte Carlo (MCMC) imputation methods. We found that the MCMC and propensity score multiple imputation approaches are, in general, superior to the other imputation methods for the configurations and training-sample sizes we considered.     

Sequential imputation for models with latent variables assuming latent ignorability

Models that involve an outcome variable, covariates, and latent variables are frequently the target for estimation and inference. The presence of missing covariate or outcome data presents a challenge, particularly when missingness depends on the latent variables. This missingness mechanism is called latent ignorable or latent missing at random and is a generalisation of missing at random. Several authors have previously proposed approaches for handling latent ignorable missingness, but these methods rely on prior specification of the joint distribution for the complete data. In practice, specifying the joint distribution can be difficult and/or restrictive. We develop a novel sequential imputation procedure for imputing covariate and outcome data for models with latent variables under latent ignorable missingness. The proposed method does not require a joint model; rather, we use results under a joint model to inform imputation with less restrictive modelling assumptions. We discuss identifiability and convergence‐related issues, and simulation results are presented in several modelling settings. The method is motivated and illustrated by a study of head and neck cancer recurrence. Imputing missing data for models with latent variables under latent‐dependent missingness without specifying a full joint model.     

Multiple Imputation of Predictor Variables Using Generalized Additive Models

The sensitivity of multiple imputation methods to deviations from their distributional assumptions is investigated using simulations, where the parameters of scientific interest are the coefficients of a linear regression model, and values in predictor variables are missing at random. The performance of a newly proposed imputation method based on generalized additive models for location, scale, and shape (GAMLSS) is investigated. Although imputation methods based on predictive mean matching are virtually unbiased, they suffer from mild to moderate under-coverage, even in the experiment where all variables are jointly normal distributed. The GAMLSS method features better coverage than currently available methods.     

Empirical likelihood confidence intervals under imputation for missing survey data from stratified simple random sampling

Missing observations due to non‐response are commonly encountered in data collected from sample surveys. The focus of this article is on item non‐response which is often handled by filling in (or imputing) missing values using the observed responses (donors). Random imputation (single or fractional) is used within homogeneous imputation classes that are formed on the basis of categorical auxiliary variables observed on all the sampled units. A uniform response rate within classes is assumed, but that rate is allowed to vary across classes. We construct confidence intervals (CIs) for a population parameter that is defined as the solution to a smooth estimating equation with data collected using stratified simple random sampling. The imputation classes are assumed to be formed across strata. Fractional imputation with a fixed number of random draws is used to obtain an imputed estimating function. An empirical likelihood inference method under the fractional imputation is proposed and its asymptotic properties are derived. Two asymptotically correct bootstrap methods are developed for constructing the desired CIs. In a simulation study, the proposed bootstrap methods are shown to outperform traditional bootstrap methods and some non‐bootstrap competitors under various simulation settings. The Canadian Journal of Statistics 47: 281–301; 2019 © 2019 Statistical Society of Canada     

A multiple imputation method for incomplete correlated ordinal data using multivariate probit models

The multiple imputation technique has proven to be a useful tool in missing data analysis. We propose a Markov chain Monte Carlo method to conduct multiple imputation for incomplete correlated ordinal data using the multivariate probit model. We conduct a thorough simulation study to compare the performance of our proposed method with two available imputation methods – multivariate normal-based and chain equation methods for various missing data scenarios. For illustration, we present an application using the data from the smoking cessation treatment study for low-income community corrections smokers.     

A stochastic variant of the EM algorithm to fit mixed (discrete and continuous) longitudinal data with nonignorable missingness

Abstract

In longitudinal studies data are collected on the same set of units for more than one occasion. In medical studies it is very common to have mixed Poisson and continuous longitudinal data. In such studies, for different reasons, some intended measurements might not be available resulting in a missing data setting. When the probability of missingness is related to the missing values, the missingness mechanism is termed nonrandom. The stochastic expectation-maximization (SEM) algorithm and the parametric fractional imputation (PFI) method are developed to handle nonrandom missingness in mixed discrete and continuous longitudinal data assuming different covariance structures for the continuous outcome. The proposed techniques are evaluated using simulation studies. Also, the proposed techniques are applied to the interstitial cystitis data base (ICDB) data.     

A multiple imputation approach to nonlinear mixed-effects models with covariate measurement errors and missing values

In longitudinal studies, nonlinear mixed-effects models have been widely applied to describe the intra- and the inter-subject variations in data. The inter-subject variation usually receives great attention and it may be partially explained by time-dependent covariates. However, some covariates may be measured with substantial errors and may contain missing values. We proposed a multiple imputation method, implemented by a Markov Chain Monte-Carlo method along with Gibbs sampler, to address the covariate measurement errors and missing data in nonlinear mixed-effects models. The multiple imputation method is illustrated in a real data example. Simulation studies show that the multiple imputation method outperforms the commonly used naive methods.     

Using data augmentation to correct for non-ignorable non-response when surrogate data are available: an application to the distribution of hourly pay

Summary.  The paper develops a data augmentation method to estimate the distribution function of a variable, which is partially observed, under a non-ignorable missing data mechanism, and where surrogate data are available. An application to the estimation of hourly pay distributions using UK Labour Force Survey data provides the main motivation. In addition to considering a standard parametric data augmentation method, we consider the use of hot deck imputation methods as part of the data augmentation procedure to improve the robustness of the method. The method proposed is compared with standard methods that are based on an ignorable missing data mechanism, both in a simulation study and in the Labour Force Survey application. The focus is on reducing bias in point estimation, but variance estimation using multiple imputation is also considered briefly.     

Comparison of several imputation methods for missing baseline data in propensity scores analysis of binary outcome

We performed a simulation study comparing the statistical properties of the estimated log odds ratio from propensity scores analyses of a binary response variable, in which missing baseline data had been imputed using a simple imputation scheme (Treatment Mean Imputation), compared with three ways of performing multiple imputation (MI) and with a Complete Case analysis. MI that included treatment (treated/untreated) and outcome (for our analyses, outcome was adverse event [yes/no]) in the imputer's model had the best statistical properties of the imputation schemes we studied. MI is feasible to use in situations where one has just a few outcomes to analyze. We also found that Treatment Mean Imputation performed quite well and is a reasonable alternative to MI in situations where it is not feasible to use MI. Treatment Mean Imputation performed better than MI methods that did not include both the treatment and outcome in the imputer's model. Copyright © 2009 John Wiley & Sons, Ltd.     

Latent class based multiple imputation approach for missing categorical data

In this paper we propose a latent class based multiple imputation approach for analyzing missing categorical covariate data in a highly stratified data model. In this approach, we impute the missing data assuming a latent class imputation model and we use likelihood methods to analyze the imputed data. Via extensive simulations, we study its statistical properties and make comparisons with complete case analysis, multiple imputation, saturated log-linear multiple imputation and the Expectation–Maximization approach under seven missing data mechanisms (including missing completely at random, missing at random and not missing at random). These methods are compared with respect to bias, asymptotic standard error, type I error, and 95% coverage probabilities of parameter estimates. Simulations show that, under many missingness scenarios, latent class multiple imputation performs favorably when jointly considering these criteria. A data example from a matched case–control study of the association between multiple myeloma and polymorphisms of the Inter-Leukin 6 genes is considered.     

Multiple imputation: an alternative to top coding for statistical disclosure control

Summary.  Top coding of extreme values of variables like income is a common method of statistical disclosure control, but it creates problems for the data analyst. The paper proposes two alternative methods to top coding for statistical disclosure control that are based on multiple imputation. We show in simulation studies that the multiple-imputation methods provide better inferences of the publicly released data than top coding, using straightforward multiple-imputation methods of analysis, while maintaining good statistical disclosure control properties. We illustrate the methods on data from the 1995 Chinese household income project.     

Missing data methods for arbitrary missingness with small samples

Missing data are a prevalent and widespread data analytic issue and previous studies have performed simulations to compare the performance of missing data methods in various contexts and for various models; however, one such context that has yet to receive much attention in the literature is the handling of missing data with small samples, particularly when the missingness is arbitrary. Prior studies have either compared methods for small samples with monotone missingness commonly found in longitudinal studies or have investigated the performance of a single method to handle arbitrary missingness with small samples but studies have yet to compare the relative performance of commonly implemented missing data methods for small samples with arbitrary missingness. This study conducts a simulation study to compare and assess the small sample performance of maximum likelihood, listwise deletion, joint multiple imputation, and fully conditional specification multiple imputation for a single-level regression model with a continuous outcome. Results showed that, provided assumptions are met, joint multiple imputation unanimously performed best of the methods examined in the conditions under study.     

Validity and efficiency in analyzing ordinal responses with missing observations

This article addresses issues in creating public-use data files in the presence of missing ordinal responses and subsequent statistical analyses of the dataset by users. The authors propose a fully efficient fractional imputation (FI) procedure for ordinal responses with missing observations. The proposed imputation strategy retrieves the missing values through the full conditional distribution of the response given the covariates and results in a single imputed data file that can be analyzed by different data users with different scientific objectives. Two most critical aspects of statistical analyses based on the imputed data set,  validity  and  efficiency, are examined through regression analysis involving the ordinal response and a selected set of covariates. It is shown through both theoretical development and simulation studies that, when the ordinal responses are missing at random, the proposed FI procedure leads to valid and highly efficient inferences as compared to existing methods. Variance estimation using the fractionally imputed data set is also discussed. The Canadian Journal of Statistics 48: 138–151; 2020 © 2019 Statistical Society of Canada     

Efficient estimation in a regression model with missing responses

This article examines methods to efficiently estimate the mean response in a linear model with an unknown error distribution under the assumption that the responses are missing at random. We show how the asymptotic variance is affected by the estimator of the regression parameter, and by the imputation method. To estimate the regression parameter, the ordinary least squares is efficient only if the error distribution happens to be normal. If the errors are not normal, then we propose a one step improvement estimator or a maximum empirical likelihood estimator to efficiently estimate the parameter.To investigate the imputation’s impact on the estimation of the mean response, we compare the listwise deletion method and the propensity score method (which do not use imputation at all), and two imputation methods. We demonstrate that listwise deletion and the propensity score method are inefficient. Partial imputation, where only the missing responses are imputed, is compared to full imputation, where both missing and non-missing responses are imputed. Our results reveal that, in general, full imputation is better than partial imputation. However, when the regression parameter is estimated very poorly, the partial imputation will outperform full imputation. The efficient estimator for the mean response is the full imputation estimator that utilizes an efficient estimator of the parameter.     

Nonparametric methods for the estimation of imputation uncertainty

It is cleared in recent researches that the raising of missing values in datasets is inevitable. Imputation of missing data is one of the several methods which have been introduced to overcome this issue. Imputation techniques are trying to answer the case of missing data by covering missing values with reasonable estimates permanently. There are a lot of benefits for these procedures rather than their drawbacks. The operation of these methods has not been clarified, which means that they provide mistrust among analytical results. One approach to evaluate the outcomes of the imputation process is estimating uncertainty in the imputed data. Nonparametric methods are appropriate to estimating the uncertainty when data are not followed by any particular distribution. This paper deals with a nonparametric method for estimation and testing the significance of the imputation uncertainty, which is based on Wilcoxon test statistic, and which could be employed for estimating the precision of the imputed values created by imputation methods. This proposed procedure could be employed to judge the possibility of the imputation process for datasets, and to evaluate the influence of proper imputation methods when they are utilized to the same dataset. This proposed approach has been compared with other nonparametric resampling methods, including bootstrap and jackknife to estimate uncertainty in the imputed data under the Bayesian bootstrap imputation method. The ideas supporting the proposed method are clarified in detail, and a simulation study, which indicates how the approach has been employed in practical situations, is illustrated.