Parametric fractional imputation for nonignorable missing data

Parameter estimation with missing data is a frequently encountered problem in statistics. Imputation is often used to facilitate the parameter estimation by simply applying the complete-sample estimators to the imputed dataset.In this article, we consider the problem of parameter estimation with nonignorable missing data using the approach of parametric fractional imputation proposed by Kim (2011). Using the fractional weights, the E-step of the EM algorithm can be approximated by the weighted mean of the imputed data likelihood where the fractional weights are computed from the current value of the parameter estimates. Calibration fractional imputation is also considered as a way for improving the Monte Carlo approximation in the fractional imputation. Variance estimation is also discussed. Results from two simulation studies are presented to compare the proposed method with the existing methods. A real data example from the Korea Labor and Income Panel Survey (KLIPS) is also presented.     

缺失偏态数据下线性回归模型的统计推断

研究缺失偏态数据下线性回归模型的参数估计问题,针对缺失偏态数据,为克服样本分布扭曲缺点和提高模型的回归系数、尺度参数和偏度参数的估计效果,提出了一种适合偏态数据下线性回归模型中缺失数据的修正回归插补方法.通过随机模拟和实例研究,并与均值插补、回归插补、随机回归插补方法比较,结果表明所提出的修正回归插补方法是有效可行的.     

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.     

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.     

Nonparametric conditional mean imputation

Imputation is a much used method for handling missing data. It is appealing as it separates the missing data part of the analysis, which is handled by imputation, and the estimation part, which is handled by complete data methods. Most imputation methods, however, either rely on strict parametric assumptions or are rather ad hoc in which case they often only work approximately under even stricter assumptions. In this paper a non-parametric imputation method is proposed. Since it is non-parametric it works under quite general assumptions. In particular, a model for the complete data is not required in the imputation step, and the complete data method used after the imputation may be a general estimating equation for estimating a finite-dimensional parameter. Large sample results for the resulting estimator are given.     

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.     

Statistical inference under imputation for proportional hazard model with missing covariates

Missing covariate data are common in biomedical studies. In this article, by using the non parametric kernel regression technique, a new imputation approach is developed for the Cox-proportional hazard regression model with missing covariates. This method achieves the same efficiency as the fully augmented weighted estimators (Qi et al. 2005. Journal of the American Statistical Association, 100:1250) and has a simpler form. The asymptotic properties of the proposed estimator are derived and analyzed. The comparisons between the proposed imputation method and several other existing methods are conducted via a number of simulation studies and a mouse leukemia data.     

A mixed effects model for analyzing area under the curve of longitudinally measured biomarkers with missing data

A simple approach for analyzing longitudinally measured biomarkers is to calculate summary measures such as the area under the curve (AUC) for each individual and then compare the mean AUC between treatment groups using methods such as t test. This two-step approach is difficult to implement when there are missing data since the AUC cannot be directly calculated for individuals with missing measurements. Simple methods for dealing with missing data include the complete case analysis and imputation. A recent study showed that the estimated mean AUC difference between treatment groups based on the linear mixed model (LMM), rather than on individually calculated AUCs by simple imputation, has negligible bias under random missing assumptions and only small bias when missing is not at random. However, this model assumes the outcome to be normally distributed, which is often violated in biomarker data. In this paper, we propose to use a LMM on log-transformed biomarkers, based on which statistical inference for the ratio, rather than difference, of AUC between treatment groups is provided. The proposed method can not only handle the potential baseline imbalance in a randomized trail but also circumvent the estimation of the nuisance variance parameters in the log-normal model. The proposed model is applied to a recently completed large randomized trial studying the effect of nicotine reduction on biomarker exposure of smokers.     

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.     

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     

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.     

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.     

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.     

A comparison of various software tools for dealing with missing data via imputation

In real-life situations, we often encounter data sets containing missing observations. Statistical methods that address missingness have been extensively studied in recent years. One of the more popular approaches involves imputation of the missing values prior to the analysis, thereby rendering the data complete. Imputation broadly encompasses an entire scope of techniques that have been developed to make inferences about incomplete data, ranging from very simple strategies (e.g. mean imputation) to more advanced approaches that require estimation, for instance, of posterior distributions using Markov chain Monte Carlo methods. Additional complexity arises when the number of missingness patterns increases and/or when both categorical and continuous random variables are involved. Implementation of routines, procedures, or packages capable of generating imputations for incomplete data are now widely available. We review some of these in the context of a motivating example, as well as in a simulation study, under two missingness mechanisms (missing at random and missing not at random). Thus far, evaluation of existing implementations have frequently centred on the resulting parameter estimates of the prescribed model of interest after imputing the missing data. In some situations, however, interest may very well be on the quality of the imputed values at the level of the individual – an issue that has received relatively little attention. In this paper, we focus on the latter to provide further insight about the performance of the different routines, procedures, and packages in this respect.     

Comparison of alternative imputation methods for ordinal data

In this article, we compare alternative missing imputation methods in the presence of ordinal data, in the framework of CUB (Combination of Uniform and (shifted) Binomial random variable) models. Various imputation methods are considered, as are univariate and multivariate approaches. The first step consists of running a simulation study designed by varying the parameters of the CUB model, to consider and compare CUB models as well as other methods of missing imputation. We use real datasets on which to base the comparison between our approach and some general methods of missing imputation for various missing data mechanisms.     

Bayesian analysis of multivariate t linear mixed models with missing responses at random

The multivariate t linear mixed model (MtLMM) has been recently proposed as a robust tool for analysing multivariate longitudinal data with atypical observations. Missing outcomes frequently occur in longitudinal research even in well controlled situations. As a powerful alternative to the traditional expectation maximization based algorithm employing single imputation, we consider a Bayesian analysis of the MtLMM to account for the uncertainties of model parameters and missing outcomes through multiple imputation. An inverse Bayes formulas sampler coupled with Metropolis-within-Gibbs scheme is used to effectively draw the posterior distributions of latent data and model parameters. The techniques for multiple imputation of missing values, estimation of random effects, prediction of future responses, and diagnostics of potential outliers are investigated as well. The proposed methodology is illustrated through a simulation study and an application to AIDS/HIV data.     

基于随机森林模型的分类数据缺失值插补

缺失数据是影响调查问卷数据质量的重要因素,对调查问卷中的缺失值进行插补可以显著提高调查数据的质量。调查问卷的数据类型多以分类型数据为主,数据挖掘技术中的分类算法是处理属性分类问题的常用方法,随机森林模型是众多分类算法中精度较高的方法之一。将随机森林模型引入调查问卷缺失数据的插补研究中,提出了基于随机森林模型的分类数据缺失值插补方法,并根据不同的缺失模式探讨了相应的插补步骤。通过与其它方法的实证模拟比较,表明随机森林插补法得到的插补值准确度更优、可信度更高。     

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.     

A comparison study of nonparametric imputation methods

Consider estimation of a population mean of a response variable when the observations are missing at random with respect to the covariate. Two common approaches to imputing the missing values are the nonparametric regression weighting method and the Horvitz-Thompson (HT) inverse weighting approach. The regression approach includes the kernel regression imputation and the nearest neighbor imputation. The HT approach, employing inverse kernel-estimated weights, includes the basic estimator, the ratio estimator and the estimator using inverse kernel-weighted residuals. Asymptotic normality of the nearest neighbor imputation estimators is derived and compared to kernel regression imputation estimator under standard regularity conditions of the regression function and the missing pattern function. A comprehensive simulation study shows that the basic HT estimator is most sensitive to discontinuity in the missing data patterns, and the nearest neighbors estimators can be insensitive to missing data patterns unbalanced with respect to the distribution of the covariate. Empirical studies show that the nearest neighbor imputation method is most effective among these imputation methods for estimating a finite population mean and for classifying the species of the iris flower data.     

Variance estimation when donor imputation is used to fill in missing values

Donor imputation is frequently used in surveys. However, very few variance estimation methods that take into account donor imputation have been developed in the literature. This is particularly true for surveys with high sampling fractions using nearest donor imputation, often called nearest‐neighbour imputation. In this paper, the authors develop a variance estimator for donor imputation based on the assumption that the imputed estimator of a domain total is approximately unbiased under an imputation model; that is, a model for the variable requiring imputation. Their variance estimator is valid, irrespective of the magnitude of the sampling fractions and the complexity of the donor imputation method, provided that the imputation model mean and variance are accurately estimated. They evaluate its performance in a simulation study and show that nonparametric estimation of the model mean and variance via smoothing splines brings robustness with respect to imputation model misspecifications. They also apply their variance estimator to real survey data when nearest‐neighbour imputation has been used to fill in the missing values. The Canadian Journal of Statistics 37: 400–416; 2009 © 2009 Statistical Society of Canada