Functional and Structural Methods with Mixed Measurement Error and Misclassification in Covariates

Misclassification simulation extrapolation method for a Weibull accelerated failure time model

The problem of misclassification in covariates is ubiquitous in survival data and often leads to biased estimates. The misclassification simulation extrapolation method is a popular method to correct this bias. However, its impact on Weibull accelerated failure time models has not been studied. In this paper, we study the bias caused by misclassification in one or more binary covariates in Weibull accelerated failure time models and explore the use of the misclassification simulation extrapolation in correcting for this bias, along with its asymptotic properties. Simulation studies are carried out to investigate the numerical properties of the resulting estimator for finite samples. The proposed method is then applied to colon cancer data obtained from the cancer registry at Memorial Sloan Kettering Cancer Center.

Mediation analysis in the presence of continuous exposure measurement error

The difference method is used in mediation analysis to quantify the extent to which a mediator explains the mechanisms underlying the pathway between an exposure and an outcome. In many health science studies, the exposures are almost never measured without error, which can result in biased effect estimates. This article investigates methods for mediation analysis when a continuous exposure is mismeasured. Under a linear exposure measurement error model, we prove that the bias of indirect effect and mediation proportion can go in either direction but the mediation proportion is usually be less biased when the associations between the exposure and its error-prone counterpart are similar with and without adjustment for the mediator. We further propose methods to adjust for exposure measurement error with continuous and binary outcomes. The proposed approaches require a main study/validation study design where in the validation study, data are available for characterizing the relationship between the true exposure and its error-prone counterpart. The proposed approaches are then applied to the Health Professional Follow-up Study, 1986-2016, to investigate the impact of body mass index (BMI) as a mediator for mediating the effect of physical activity on the risk of cardiovascular diseases. Our results reveal that physical activity is significantly associated with a lower risk of cardiovascular disease incidence, and approximately half of the total effect of physical activity is mediated by BMI after accounting for exposure measurement error. Extensive simulation studies are conducted to demonstrate the validity and efficiency of the proposed approaches in finite samples.

Logistic regression with correlated measurement error and misclassification in covariates

Many areas of research, such as nutritional epidemiology, may encounter measurement errors of continuous covariates and misclassification of categorical variables when modeling. It is well known that ignoring measurement errors or misclassification can lead to biased results. But most research has focused on solving these two problems separately. Addressing both measurement error and misclassification simultaneously in a single analysis is less actively studied. In this article, we propose a new correction method for a logistic regression to handle correlated error variables involved in multivariate continuous covariates and misclassification in a categorical variable simultaneously. It is not computationally intensive since a closed-form of the approximate likelihood function conditional on observed covariates is derived. The asymptotic normality of this proposed estimator is established under regularity conditions and its finite-sample performance is empirically examined by simulation studies. We apply this new estimation method to handle measurement error in some nutrients of interest and misclassification of a categorical variable named physical activity in the European Prospective Investigation into Cancer and Nutrition-InterAct Study data. Analyses show that fruit is negatively associated with type 2 diabetes for a group of women doing active physical activity, protein has positive association with type 2 diabetes for the group of less active physical activity, and actual physical activity has a greater effect on reducing the risk of type 2 diabetes than observed physical activity.

Estimation of the average treatment effect with variable selection and measurement error simultaneously addressed for potential confounders

In the framework of causal inference, the inverse probability weighting estimation method and its variants have been commonly employed to estimate the average treatment effect. Such methods, however, are challenged by the presence of irrelevant pre-treatment variables and measurement error. Ignoring these features and naively applying the usual inverse probability weighting estimation procedures may typically yield biased inference results. In this article, we develop an inference method for estimating the average treatment effect with those features taken into account. We establish theoretical properties for the resulting estimator and carry out numerical studies to assess the finite sample performance of the proposed estimator.

Zero-inflated poisson models with measurement error in the response

Zero-inflated count data arise frequently from genomics studies. Analysis of such data is often based on a mixture model which facilitates excess zeros in combination with a Poisson distribution, and various inference methods have been proposed under such a model. Those analysis procedures, however, are challenged by the presence of measurement error in count responses. In this article, we propose a new measurement error model to describe error-contaminated count data. We show that ignoring the measurement error effects in the analysis may generally lead to invalid inference results, and meanwhile, we identify situations where ignoring measurement error can still yield consistent estimators. Furthermore, we propose a Bayesian method to address the effects of measurement error under the zero-inflated Poisson model and discuss the identifiability issues. We develop a data-augmentation algorithm that is easy to implement. Simulation studies are conducted to evaluate the performance of the proposed method. We apply our method to analyze the data arising from a prostate adenocarcinoma genomics study. This article is protected by copyright. All rights reserved.

A Bayesian approach for estimating the partial potential impact fraction with exposure measurement error under a main study/internal validation design

The partial potential impact fraction describes the proportion of disease cases that can be prevented if the distribution of modifiable continuous exposures is shifted in a population, while other risk factors are not modified. It is a useful quantity for evaluating the burden of disease in epidemiologic and public health studies. When exposures are measured with error, the partial potential impact fraction estimates may be biased, which necessitates methods to correct for the exposure measurement error. Motivated by the health professionals follow-up study, we develop a Bayesian approach to adjust for exposure measurement error when estimating the partial potential impact fraction under the main study/internal validation study design. We adopt the reclassification approach that leverages the strength of the main study/internal validation study design and clarifies transportability assumptions for valid inference. We assess the finite-sample performance of both the point and credible interval estimators via extensive simulations and apply the proposed approach in the health professionals follow-up study to estimate the partial potential impact fraction for colorectal cancer incidence under interventions exploring shifting the distributions of red meat, alcohol, and/or folate intake.

Estimation and inference for the population attributable risk in the presence of misclassification

Because it describes the proportion of disease cases that could be prevented if an exposure were entirely eliminated from a target population as a result of an intervention, estimation of the population attributable risk (PAR) has become an important goal of public health research. In epidemiologic studies, categorical covariates are often misclassified. We present methods for obtaining point and interval estimates of the PAR and the partial PAR (pPAR) in the presence of misclassification, filling an important existing gap in public health evaluation methods. We use a likelihood-based approach to estimate parameters in the models for the disease and for the misclassification process, under main study/internal validation study and main study/external validation study designs, and various plausible assumptions about transportability. We assessed the finite sample perf ormance of this method via a simulation study, and used it to obtain corrected point and interval estimates of the pPAR for high red meat intake and alcohol intake in relation to colorectal cancer incidence in the HPFS, where we found that the estimated pPAR for the two risk factors increased by up to 317% after correcting for bias due to misclassification.

Marginal analysis of bivariate mixed responses with measurement error and misclassification

Bivariate responses with mixed continuous and binary variables arise commonly in applications such as clinical trials and genetic studies. Statistical methods based on jointly modeling continuous and binary variables have been available. However, such methods ignore the effects of response mismeasurement, a ubiquitous feature in applications. It has been well studied that in many settings, ignorance of mismeasurement in variables usually results in biased estimation. In this paper, we consider the setting with a bivariate outcome vector which contains a continuous component and a binary component both subject to mismeasurement. We propose estimating equation approaches to handle measurement error in the continuous response and misclassification in the binary response simultaneously. The proposed estimators are consistent and robust to certain model misspecification, provided regularity conditions. Extensive simulation studies confirm that the proposed methods successfully correct the biases resulting from the error-in-variables under various settings. The proposed methods are applied to analyze the outbred Carworth Farms White mice data arising from a genome-wide association study.

Genetic association studies with bivariate mixed responses subject to measurement error and misclassification

In genetic association studies, mixed effects models have been widely used in detecting the pleiotropy effects which occur when one gene affects multiple phenotype traits. In particular, bivariate mixed effects models are useful for describing the association of a gene with a continuous trait and a binary trait. However, such models are inadequate to feature the data with response mismeasurement, a characteristic that is often overlooked. It has been well studied that in univariate settings, ignorance of mismeasurement in variables usually results in biased estimation. In this paper, we consider the setting with a bivariate outcome vector which contains a continuous component and a binary component both subject to mismeasurement. We propose an induced likelihood approach and an EM algorithm method to handle measurement error in continuous response and misclassification in binary response simultaneously. Simulation studies confirm that the proposed methods successfully remove the bias induced from the response mismeasurement.

Approximate maximum likelihood estimation for logistic regression with covariate measurement error

In nutritional epidemiology, dietary intake assessed with a food frequency questionnaire is prone to measurement error. Ignoring the measurement error in covariates causes estimates to be biased and leads to a loss of power. In this paper, we consider an additive error model according to the characteristics of the European Prospective Investigation into Cancer and Nutrition (EPIC)-InterAct Study data, and derive an approximate maximum likelihood estimation (AMLE) for covariates with measurement error under logistic regression. This method can be regarded as an adjusted version of regression calibration and can provide an approximate consistent estimator. Asymptotic normality of this estimator is established under regularity conditions, and simulation studies are conducted to empirically examine the finite sample performance of the proposed method. We apply AMLE to deal with measurement errors in some interested nutrients of the EPIC-InterAct Study under a sensitivity analysis framework.

MALMEM: model averaging in linear measurement error models

We develop model averaging estimation in the linear regression model where some covariates are subject to measurement error. The absence of the true covariates in this framework makes the calculation of the standard residual-based loss function impossible. We take advantage of the explicit form of the parameter estimators and construct a weight choice criterion. It is asymptotically equivalent to the unknown model average estimator minimizing the loss function. When the true model is not included in the set of candidate models, the method achieves optimality in terms of minimizing the relative loss, whereas, when the true model is included, the method estimates the model parameter with root n rate. Simulation results in comparison with existing Bayesian information criterion and Akaike information criterion model selection and model averaging methods strongly favour our model averaging method. The method is applied to a study on health.

Analysis of noisy survival data with graphical proportional hazards measurement error models

In survival data analysis, the Cox proportional hazards (PH) model is perhaps the most widely used model to feature the dependence of survival times on covariates. While many inference methods have been developed under such a model or its variants, those models are not adequate for handling data with complex structured covariates. High-dimensional survival data often entail several features: (1) many covariates are inactive in explaining the survival information, (2) active covariates are associated in a network structure, and (3) some covariates are error-contaminated. To hand such kinds of survival data, we propose graphical PH measurement error models and develop inferential procedures for the parameters of interest. Our proposed models significantly enlarge the scope of the usual Cox PH model and have great flexibility in characterizing survival data. Theoretical results are established to justify the proposed methods. Numerical studies are conducted to assess the performance of the proposed methods.

STRATOS guidance document on measurement error and misclassification of variables in observational epidemiology: Part 2-More complex methods of adjustment and advanced topics

We continue our review of issues related to measurement error and misclassification in epidemiology. We further describe methods of adjusting for biased estimation caused by measurement error in continuous covariates, covering likelihood methods, Bayesian methods, moment reconstruction, moment-adjusted imputation, and multiple imputation. We then describe which methods can also be used with misclassification of categorical covariates. Methods of adjusting estimation of distributions of continuous variables for measurement error are then reviewed. Illustrative examples are provided throughout these sections. We provide lists of available software for implementing these methods and also provide the code for implementing our examples in the Supporting Information. Next, we present several advanced topics, including data subject to both classical and Berkson error, modeling continuous exposures with measurement error, and categorical exposures with misclassification in the same model, variable selection when some of the variables are measured with error, adjusting analyses or design for error in an outcome variable, and categorizing continuous variables measured with error. Finally, we provide some advice for the often met situations where variables are known to be measured with substantial error, but there is only an external reference standard or partial (or no) information about the type or magnitude of the error.

Emergency department utilization and resuscitation rate among patients receiving maintenance hemodialysis

BACKGROUND

End-stage renal disease (ESRD) is a growing global health concern with increased disease burden and high medical costs. Utilization of the emergency department (ED) among dialyzed patients and the associated risk factors remain unknown.

METHODS

Participants of this study, selected from the National Health Insurance Database in Taiwan, were aged 19-90 years and received maintenance hemodialysis from January 1, 2010, to December 31, 2010. A control group consisting of individuals who did not receive dialysis, selected from the same data source, were matched for age, sex, and the Charlson Comorbidity Index (CCI). Subgroup analysis with hemodialysis frequency was also performed. ED utilization among enrolled individuals was assessed in 2012. Generalized estimating equations with multiple variable adjustments were used to identify risk factors associated with resuscitation during ED visits.

RESULTS

One group of 2985 individuals who received maintenance hemodialysis, and another group of 2985 patients that did not receive hemodialysis, between January 1, 2010, and December 31, 2010, were included in this study. There were 4822 ED visits in the hemodialysis group, and 1755 ED visits in the non-dialysis group between January 1, 2012, and December 31, 2012. Analysis of multivariable generalized estimating equations identified the risk associated with resuscitation during ED visits to be greater in individuals who were receiving maintenance hemodialysis, aged older than 55 years, hospitalized in the past year, and assigned first and second degree of triage.

CONCLUSION

Patients receiving maintenance hemodialysis had higher ED utilization and a significantly higher risk of resuscitation during ED visits than those without hemodialysis.

Parametric Regression Analysis with Covariate Misclassification in Main Study/Validation Study Designs

Measurement error and misclassification have long been a concern in many fields, including medicine, administrative health care data, epidemiology, and survey sampling. It is known that measurement error and misclassification may seriously degrade the quality of estimation and inference, and should be avoided whenever possible. However, in practice, it is inevitable that measurements contain error for a variety of reasons. It is thus necessary to develop statistical strategies to cope with this issue. Although many inference methods have been proposed in the literature to address mis-measurement effects, some important issues remain unexplored. Typically, it is generally unclear how the available methods may perform relative to each other. In this paper, capitalizing on the unique feature of discrete variables, we consider settings with misclassified binary covariates and investigate issues concerning covariate misclassification; our development parallels available strategies for handling measurement error in continuous covariates. Under a unified framework, we examine a number of valid inferential procedures for practical settings where a validation study, either internal or external, is available besides a main study. Furthermore, we compare the relative performance of these methods and make practical recommendations.

An Explorative Study on Estimating Local Accuracies in Land-Cover Information Using Logistic Regression and Class-Heterogeneity-Stratified Data

It is increasingly recognized that classification accuracy should be characterized locally at the level of individual pixels to depict its spatial variability to better inform users and producers of land-cover information than by conventional error-matrix-based methods. Local or per-pixel accuracy is usually estimated through empirical modelling, such as logistic regression, which often proceeds in a class-aggregated or a class-stratified way, with the latter being generally more accurate due to its accommodation for between-class inhomogeneity in accuracy-context relations. As an extension to class-stratified modelling, class-heterogeneity-stratified modelling, in which logistic models are built separately for contextually heterogeneous vs. homogeneous sub-strata in individual strata of map classes, is proposed in this paper for proper handling of within-class inhomogeneity in accuracy-context relations to increase accuracy of estimation. Unlike in existing literature where sampling is usually approached separately, the double-stratification method is also adopted in sampling design so that more sample data are likely allocated to heterogeneous sub-strata (which are more prone to misclassifications than homogeneous ones). This class-heterogeneity-stratified method furnished for sampling and modelling jointly thus constitutes an integrative framework for accuracy estimation and information refinement. As the first step in building up such a framework, this paper investigates the proposed double-stratification method’s performance and sensitivity to sample size regarding local accuracy estimation in comparison with those of existing methods through a case study concerning Globeland30 2010 land cover over Wuhan, China. A detailed review of existing methods for analyses, estimation, and use of local accuracy was provided, helping to put the proposed research in a broader context. Candidate explanatory variables for logistic regression included sample pixels’ map classes, positions, and contextual features that were computed in different-sized moving windows. Relative performances of these methods were evaluated based on an independent reference sample, with all methods found reliable. It was confirmed that the proposed method is in general the most accurate, as observed with varying sample sizes. The proposed method’s competitive performance is thus proved, reinforcing its potential for information refinement. Extensions to and uncertainty aspects of the proposed method were discussed, with further research proposed.

Clustering in General Measurement Error Models

This paper is dedicated to the memory of Peter G. Hall. It concerns a deceptively simple question: if one observes variables corrupted with measurement error of possibly very complex form, can one recreate asymptotically the clusters that would have been found had there been no measurement error? We show that the answer is yes, and that the solution is surprisingly simple and general. The method itself is to simulate, by computer, realizations with the same distribution as that of the true variables, and then to apply clustering to these realizations. Technically, we show that if one uses K-means clustering or any other risk minimizing clustering, and a multivariate deconvolution device with certain smoothness and convergence properties, then, in the limit, the cluster means based on our method converge to the same cluster means as if there is no measurement error. Along with the method and its technical justification, we analyze two important nutrition data sets, finding patterns that make sense nutritionally.

Causal inference with measurement error in outcomes: Bias analysis and estimation methods

Inverse probability weighting estimation has been popularly used to consistently estimate the average treatment effect. Its validity, however, is challenged by the presence of error-prone variables. In this paper, we explore the inverse probability weighting estimation with mismeasured outcome variables. We study the impact of measurement error for both continuous and discrete outcome variables and reveal interesting consequences of the naive analysis which ignores measurement error. When a continuous outcome variable is mismeasured under an additive measurement error model, the naive analysis may still yield a consistent estimator; when the outcome is binary, we derive the asymptotic bias in a closed-form. Furthermore, we develop consistent estimation procedures for practical scenarios where either validation data or replicates are available. With validation data, we propose an efficient method for estimation of average treatment effect; the efficiency gain is substantial relative to usual methods of using validation data. To provide protection against model misspecification, we further propose a doubly robust estimator which is consistent even when either the treatment model or the outcome model is misspecified. Simulation studies are reported to assess the performance of the proposed methods. An application to a smoking cessation dataset is presented.

Linear Model Selection when Covariates Contain Errors

Prediction precision is arguably the most relevant criterion of a model in practice and is often a sought after property. A common difficulty with covariates measured with errors is the impossibility of performing prediction evaluation on the data even if a model is completely given without any unknown parameters. We bypass this inherent difficulty by using special properties on moment relations in linear regression models with measurement errors. The end product is a model selection procedure that achieves the same optimality properties that are achieved in classical linear regression models without covariate measurement error. Asymptotically, the procedure selects the model with the minimum prediction error in general, and selects the smallest correct model if the regression relation is indeed linear. Our model selection procedure is useful in prediction when future covariates without measurement error become available, e.g., due to improved technology or better management and design of data collection procedures.

A method for sensitivity analysis to assess the effects of measurement error in multiple exposure variables using external validation data

BACKGROUND

Measurement error in self-reported dietary intakes is known to bias the association between dietary intake and a health outcome of interest such as risk of a disease. The association can be distorted further by mismeasured confounders, leading to invalid results and conclusions. It is, however, difficult to adjust for the bias in the association when there is no internal validation data.

METHODS

We proposed a method to adjust for the bias in the diet-disease association (hereafter, association), due to measurement error in dietary intake and a mismeasured confounder, when there is no internal validation data. The method combines prior information on the validity of the self-report instrument with the observed data to adjust for the bias in the association. We compared the proposed method with the method that ignores the confounder effect, and with the method that ignores measurement errors completely. We assessed the sensitivity of the estimates to various magnitudes of measurement error, error correlations and uncertainty in the literature-reported validation data. We applied the methods to fruits and vegetables (FV) intakes, cigarette smoking (confounder) and all-cause mortality data from the European Prospective Investigation into Cancer and Nutrition study.

RESULTS

Using the proposed method resulted in about four times increase in the strength of association between FV intake and mortality. For weakly correlated errors, measurement error in the confounder minimally affected the hazard ratio estimate for FV intake. The effect was more pronounced for strong error correlations.

CONCLUSIONS

The proposed method permits sensitivity analysis on measurement error structures and accounts for uncertainties in the reported validity coefficients. The method is useful in assessing the direction and quantifying the magnitude of bias in the association due to measurement errors in the confounders.