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Trivariate joint modeling for longitudinal count data, recurrent events, and a terminal event for family data has increased interest in medical studies. For example, families with Lynch syndrome (LS) are at high risk of developing colorectal cancer (CRC), where the number of polyps and the frequency of colonoscopy screening visits are highly associated with the risk of CRC among individuals and families. To assess how screening visits influence polyp detection, which in turn influences time to CRC, we propose a clustered trivariate joint model. The proposed model facilitates longitudinal count data that are zero‐inflated and over‐dispersed and invokes individual‐specific and family‐specific random effects to account for dependence among individuals and families. We formulate our proposed model as a latent Gaussian model to use the Bayesian estimation approach with the integrated nested Laplace approximation algorithm and evaluate its performance using simulation studies. Our trivariate joint model is applied to a series of 18 families from Newfoundland, with the occurrence of CRC taken as the terminal event, the colonoscopy screening visits as recurrent events, and the number of polyps detected at each visit as zero‐inflated count data with overdispersion. We showed that our trivariate model fits better than alternative bivariate models and that the cluster effects should not be ignored when analyzing family data. Finally, the proposed model enables us to quantify heterogeneity across families and individuals in polyp detection and CRC risk, thus helping to identify individuals and families who would benefit from more intensive screening visits. [ABSTRACT FROM AUTHOR]

In causal inference, the estimation of the average treatment effect is often of interest. For example, in cancer research, an interesting question is to assess the effects of the chemotherapy treatment on cancer, with the information of gene expressions taken into account. Two crucial challenges in this analysis involve addressing measurement error in gene expressions and handling noninformative gene expressions. While analytical methods have been developed to address those challenges, no user-friendly computational software packages seem to be available to implement those methods. To close this gap, we develop an R package, called AteMeVs, to estimate the average treatment effect using the inverse-probability-weighting estimation method to handle data with both measurement error and spurious variables. This developed package accommodates the method proposed by Yi and Chen (2023) as a special case, and further extends its application to a broader scope. The usage of the developed R package is illustrated by applying it to analyze a cancer dataset with information of gene expressions. [ABSTRACT FROM AUTHOR]

Modelling multivariate survival data is complicated by the complex association structure among the responses. To balance model flexibility and interpretability, we propose a semiparametric copula model to modulate multivariate survival data, with the marginal distributions of the response components described by semiparametric linear transformation models. To conduct inference about the model parameters, we develop a two‐stage maximum likelihood method and a three‐stage pseudo‐likelihood estimation procedure. We investigate the impact of model misspecification on the estimation of covariate effects and identify a scenario in which consistent estimation of the marginal parameters is retained even when the copula model is misspecified. The proposed methods are justified both theoretically and empirically. An application to a real dataset is provided to demonstrate the utility of the proposed method. [ABSTRACT FROM AUTHOR]

Research on dynamic treatment regimes has enticed extensive interest. Many methods have been proposed in the literature, which, however, are vulnerable to the presence of misclassification in covariates. In particular, although Q‐learning has received considerable attention, its applicability to data with misclassified covariates is unclear. In this article, we investigate how ignoring misclassification in binary covariates can impact the determination of optimal decision rules in randomized treatment settings, and demonstrate its deleterious effects on Q‐learning through empirical studies. We present two correction methods to address misclassification effects on Q‐learning. Numerical studies reveal that misclassification in covariates induces non‐negligible estimation bias and that the correction methods successfully ameliorate bias in parameter estimation. [ABSTRACT FROM AUTHOR]

Nancy Reid was born in September 1952 in Niagara Falls, Canada. She graduated from the University of Waterloo with a Bachelor in Mathematics and a Major in Statistics in 1974. She studied statistics at the University of British Columbia (UBC) where she obtained a Master's in Applied Mathematics in 1976, and at Stanford University where she graduated with a PhD in Statistics in 1979. After spending one year at Imperial College London visiting Sir David Cox, she joined UBC as an Assistant Professor in the Department of Mathematics, and in 1986 she moved to the University of Toronto as a faculty member in the Department of Statistics (now Statistical Sciences) where she has been ever since including serving as Chair between 1997 and 2002. At the time of writing, Nancy has authored over 100 papers and 5 books, including seminal developments in conditional inference, higher‐order asymptotics, composite likelihood, and Bayesian inference. Her outstanding contributions to statistics have been recognized nationally and internationally with many awards, including the President's Award of the Committee of Presidents of Statistical Societies (COPSS), the Gold Medal awarded by the Statistical Society of Canada (SSC), and being elected Foreign Associate of the National Academy of Sciences. In 2017, the International Statistical Review published Nancy's conversation with Ana Maria Staicu [Staicu, A. M. (2017). Interview with Nancy Reid. International Statistical Review, 85(3), 381‐403.], which had a biographical emphasis. Since then, Nancy has continued to support the discipline of statistics in important ways, such as by serving as Director of the Canadian Statistical Sciences Institute (CANSSI) (2015–2019) and Co‐chair of the Institute of Mathematical Statistics' Committee on Ethics (2018–2020). Her research activity continues to be celebrated with important awards such as Fellowship of the Royal Society of London (2018), the inaugural Hollander Distinguished Lectureship at Florida State University (2020), the Distinguished Achievement Award (and Lectureship) from COPSS (2022), and the Guy Medal in Gold from the Royal Statistical Society (2022). In May 2022, the Department of Statistical Sciences at the University of Toronto, in collaboration with CANSSI and the SSC, organized a one‐day conference, "Statistics at Its Best", in honour of Nancy's 70th birthday. This conversation took place in Toronto around the time of the event. Its focus is on Nancy's views on building a career in statistics, and the challenges and opportunities statisticians encounter within the rapidly evolving data science ecosystem. [ABSTRACT FROM AUTHOR]

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 genomic study. [ABSTRACT FROM AUTHOR]

Research of complex associations between a gene network and multiple responses has attracted increasing attention. A great challenge in analyzing genetic data is posited by the presence of the genetic network that is typically unknown. Moreover, mismeasurement of responses introduces additional complexity to distort usual inferential procedures. In this paper, we consider the problem with mixed binary and continuous responses that are subject to mismeasurement and associated with complex structured covariates. We first start with the case where data are precisely measured. We propose a generalized network structured model and develop a two‐step inferential procedure. In the first step, we employ a Gaussian graphical model to facilitate the covariates network structure, and in the second step, we incorporate the estimated graphical structure of covariates and develop an estimating equation method. Furthermore, we extend the development to accommodating mismeasured responses. We consider two cases where the information on mismeasurement is either known or estimated from a validation sample. Theoretical results are established and numerical studies are conducted to evaluate the finite sample performance of the proposed methods. We apply the proposed method to analyze the outbred Carworth Farms White mice data arising from a genome‐wide association study. [ABSTRACT FROM AUTHOR]

Autoregressive (AR) models are useful in time series analysis. Inferences under such models are distorted in the presence of measurement error, a common feature in applications. In this article, we establish analytical results for quantifying the biases of the parameter estimation in AR models if the measurement error effects are neglected. We consider two measurement error models to describe different data contamination scenarios. We propose an estimating equation approach to estimate the AR model parameters with measurement error effects accounted for. We further discuss forecasting using the proposed method. Our work is inspired by COVID-19 data, which are error-contaminated due to multiple reasons including those related to asymptomatic cases and varying incubation periods. We implement the proposed method by conducting sensitivity analyses and forecasting the fatality rate of COVID-19 over time for the four most populated provinces in Canada. The results suggest that incorporating or not incorporating measurement error effects may yield rather different results for parameter estimation and forecasting. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Classification trees are a popular machine learning tool for studying a variety of problems, including prediction, inference, risk factors identification, and risk groups classification. Classification trees are basically developed under the assumption that the response and covariate variables are accurately measured. This condition, however, is often violated in practice. Ignoring this feature commonly yields invalid analysis results. In this paper, we study the impact of mismeasured responses on the performance of standard classification trees and propose a novel classification trees algorithm for mismeasured responses. Our study is directed to settings with binary responses which are subject to mismeasurement. To address the effects of mismeasured responses, we modify the decision rules which are valid for tree building in the mismeasurement-free settings by introducing new measures for the node impurity and misclassification cost. To characterize the magnitude of mismeasurement in responses, we consider two data scenarios. In the first scenario, the mismeasurement rates are known, either from previous studies of the same nature or being set by researchers who are interested in conducting sensitivity analyses to assess the impact of mismeasured responses. In the second scenario, the mismeasurement rates are unknown and are estimated from a validation dataset which contains both accurate measurements and mismeasurements for responses. We conduct a variety of simulation studies to assess the performance of the proposed classification trees algorithm, in comparison to the usual classification trees algorithms which ignore response mismeasurement. It is demonstrated that ignoring response mismeasurement can yield seriously erroneous results and that our proposed method provides superior performance with the mismeasurement effects accommodated. To illustrate the usage of the proposed method, we analyze the data arising from the National Health and Nutrition Examination Surveys (NHANES) by conducting sensitivity analyses to assess how classification results may be affected by different misclassification costs. [ABSTRACT FROM AUTHOR]

While the impact of the COVID-19 pandemic has been widely studied, relatively fewer discussions about the sentimental reaction of the public are available. In this article, we scrape COVID-19 related tweets on the microblogging platform, Twitter, and examine the tweets from February 24, 2020 to October 14, 2020 in four Canadian cities (Toronto, Montreal, Vancouver, and Calgary) and four U.S. cities (New York, Los Angeles, Chicago, and Seattle). Applying the RoBERTa, Vader and NRC approaches, we evaluate sentiment intensity scores and visualize the results over different periods of the pandemic. Sentiment scores for the tweets concerning three anti-epidemic measures, "masks", "vaccine", and "lockdown", are computed for comparison. We explore possible causal relationships among the variables concerning tweet activities and sentiment scores of COVID-19 related tweets by integrating the echo state network method with convergent cross-mapping. Our analyses show that public sentiments about COVID-19 vary from time to time and from place to place, and are different with respect to anti-epidemic measures of "masks", "vaccines", and "lockdown". Evidence of the causal relationship is revealed for the examined variables, assuming the suggested model is feasible. [ABSTRACT FROM AUTHOR]

Data with a huge size present great challenges in modeling, inferences, and computation. In handling big data, much attention has been directed to settings with "large p small n", and relatively less work has been done to address problems with p and n being both large, though data with such a feature have now become more accessible than before, where p represents the number of variables and n stands for the sample size. The big volume of data does not automatically ensure good quality of inferences because a large number of unimportant variables may be collected in the process of gathering informative variables. To carry out valid statistical analysis, it is imperative to screen out noisy variables that have no predictive value for explaining the outcome variable. In this paper, we develop a screening method for handling large‐sized survival data, where the sample size n is large and the dimension p of covariates is of non‐polynomial order of the sample size n, or the so‐called NP‐dimension. We rigorously establish theoretical results for the proposed method and conduct numerical studies to assess its performance. Our research offers multiple extensions of existing work and enlarges the scope of high‐dimensional data analysis. The proposed method capitalizes on the connections among useful regression settings and offers a computationally efficient screening procedure. Our method can be applied to different situations with large‐scale data including genomic data. [ABSTRACT FROM AUTHOR]

The coronavirus disease 2019 (COVID‐19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), has spread stealthily and presented a tremendous threat to the public. It is important to investigate the transmission dynamics of COVID‐19 to help understand the impact of the disease on public health and the economy. In this article, we develop a new epidemic model that utilizes a set of ordinary differential equations with unknown parameters to delineate the transmission process of COVID‐19. The model accounts for asymptomatic infections as well as the lag between symptom onset and the confirmation date of infection. To reflect the transmission potential of an infected case, we derive the basic reproduction number from the proposed model. Using the daily reported number of confirmed cases, we describe an estimation procedure for the model parameters, which involves adapting the iterated filter‐ensemble adjustment Kalman filter (IF‐EAKF) algorithm. To illustrate the use of the proposed model, we examine the COVID‐19 data from Quebec for the period from 2 April 2020 to 10 May 2020 and carry out sensitivity studies under a variety of assumptions. Simulation studies are used to evaluate the performance of the proposed model under a variety of settings. [ABSTRACT FROM AUTHOR]

Multivariate regression models have been broadly used in analyzing data having multi-dimensional response variables. The use of such models is, however, impeded by the presence of measurement error and spurious variables. While data with such features are common in applications, there has been little work available concerning these features jointly. In this article, we consider variable selection under multivariate regression models with covariates subject to measurement error. To gain flexibility, we allow the dimensions of the covariate and response variables to be either fixed or diverging as the sample size increases. A new regularized method is proposed to handle both variable selection and measurement error effects for error-contaminated data. Our proposed penalized bias-corrected least squares method offers flexibility in selecting the penalty function from a class of functions with different features. Importantly, our method does not require full distributional assumptions for the associated variables, thereby broadening its applicability. We rigorously establish theoretical results and describe a computationally efficient procedure for the proposed method. Numerical studies confirm the satisfactory performance of the proposed method under finite settings, and also demonstrate deleterious effects of ignoring measurement error in inferential procedures. [ABSTRACT FROM AUTHOR]

Matrix-variate logistic regression is useful in facilitating the relationship between the binary response and complex-featured matrix-variates arising commonly from medical imaging research. However, standard inference procedures based on such a model are impaired by the presence of the response misclassification as well as inactive covariates. It is imperative to account for the misclassification effects and select active covariates when employing matrix-variate logistic regression to analyze such data. In this paper, we develop penalized unbiased estimating functions using the smoothly clipped absolute deviation (SCAD) penalty to address the sparsity of matrix-variate data as well as the response misclassification effects. The proposed methods are justified both theoretically and numerically. We analyze the Breast Cancer Wisconsin data with the proposed methods. • Investigate the effects of response misclassification under the matrix-variate model. • Develop an estimating function based method and a likelihood based method. • Discusse misclassification effects on the variable selection procedure. [ABSTRACT FROM AUTHOR]

Matrix‐variate logistic regression is useful in facilitating the relationship between the binary response and matrix‐variates, which arise commonly from medical imaging research. However, such a model is impaired by the presence of response misclassification. It is imperative to account for the misclassification effects when employing matrix‐variate logistic regression to handle such data. In this article, we develop two inferential methods that account for the misclassification effects. The first method, called an imputation method, has roots in the score function derived from the misclassification‐free context, and replaces the involved response variable with an unbiased pseudo‐response variable, i.e., expressed in terms of the observed surrogate measurement. The second method is to directly derive the likelihood function for the observed response surrogate and then conduct estimation accordingly. Our development is carried out for two settings where misclassification rates are either known or estimated from validation data. The proposed methods are justified both theoretically and empirically. We analyze the Breast Cancer Wisconsin (Prognostic) data with the proposed methods. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

In the presence of covariate measurement error, there has been extensive interest in developing estimation methods for parameters associated with various survival models, where the classical additive measurement error model is commonly used to describe the measurement error process. On the contrary, hypothesis testing has been less explored for survival data with error‐contaminated covariates. Furthermore, it is important to study the impact of misspecification of the measurement error process. In this article, we propose a "corrected" score test and a "corrected" Wald test and establish their theoretical properties. Moreover, we exploit the impact of misspecification of measurement error models on parameter estimation and hypothesis testing. Simulation studies are reported to demonstrate the finite‐sample performance of the proposed methods, and a real data example is presented to illustrate the usage of our methods. [ABSTRACT FROM AUTHOR]

Many methods have been developed for analyzing survival data which are commonly right-censored. These methods, however, are challenged by complex features pertinent to the data collection as well as the nature of data themselves. Typically, biased samples caused by left-truncation (or length-biased sampling) and measurement error often accompany survival analysis. While such data frequently arise in practice, little work has been available to simultaneously address these features. In this paper, we explore valid inference methods for handling left-truncated and right-censored survival data with measurement error under the widely used Cox model. We first exploit a flexible estimator for the survival model parameters which does not require specification of the baseline hazard function. To improve the efficiency, we further develop an augmented nonparametric maximum likelihood estimator. We establish asymptotic results and examine the efficiency and robustness issues for the proposed estimators. The proposed methods enjoy appealing features that the distributions of the covariates and of the truncation times are left unspecified. Numerical studies are reported to assess the finite sample performance of the proposed methods. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The swift spread of the novel coronavirus is largely attributed to its stealthy transmissions in which infected patients may be asymptomatic or exhibit only flu-like symptoms in the early stage. Undetected transmissions present a remarkable challenge for the containment of the virus and pose an appalling threat to the public. An urgent question is on testing of the coronavirus. In this paper, we evaluate the situation from the statistical viewpoint by discussing the accuracy of test procedures and stress the importance of rationally interpreting test results. [ABSTRACT FROM AUTHOR]

Measurement error in covariates has been extensively studied in many conventional regression settings where covariate information is typically expressed in a vector form. However, there has been little work on error-prone matrix-variate data, which commonly arise from studies with imaging, spatial-temporal structures, etc. We consider analysis of error-contaminated matrix-variate data. We particularly focus on matrix-variate logistic measurement error models. We examine the biases induced from naive analysis which ignores measurement error in matrix-variate data. Two measurement error correction methods are developed to adjust for measurement error effects. The proposed methods are justified both theoretically and empirically. We analyse an electroencephalography dataset with the proposed methods. [ABSTRACT FROM AUTHOR]

The swift spread of the novel coronavirus is largely attributed to its stealthy transmissions in which infected patients may be asymptomatic or exhibit only flu-like symptoms in the early stage. Undetected transmissions present a remarkable challenge for the containment of the virus and pose an appalling threat to the public. An urgent question is on testing of the coronavirus. In this paper, we evaluate the situation from the statistical viewpoint by discussing the accuracy of test procedures and stress the importance of rationally interpreting test results. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

COVID-19 is a disease caused by the severe acute respiratory syndrome coronavirus 2 (SARSCoV- 2) that was reported to spread in people in December 2019. Understanding epidemiological features of COVID-19 is important for the ongoing global efforts to contain the virus. As a complement to the available work, in this article we analyze the Kaggle novel coronavirus dataset of 3397 patients dated from January 22, 2020 to March 29, 2020. We employ semiparametric and nonparametric survival models as well as text mining and data visualization techniques to examine the clinical manifestations and epidemiological features of COVID-19. Our analysis shows that: (i) the median incubation time is about 5 days and older people tend to have a longer incubation period; (ii) the median time for infected people to recover is about 20 days, and the recovery time is significantly associated with age but not gender; (iii) the fatality rate is higher for older infected patients than for younger patients. [ABSTRACT FROM AUTHOR]

Causal inference has been widely conducted in various fields and many methods have been proposed for different settings. However, for noisy data with both mismeasurements and missing observations, those methods often break down. In this paper, we consider a problem that binary outcomes are subject to both missingness and misclassification, when the interest is in estimation of the average treatment effects (ATE). We examine the asymptotic biases caused by ignoring missingness and/or misclassification and establish the intrinsic connections between missingness effects and misclassification effects on the estimation of ATE. We develop valid weighted estimation methods to simultaneously correct for missingness and misclassification effects. To provide protection against model misspecification, we further propose a doubly robust correction method which yields consistent estimators when either the treatment model or the outcome model is misspecified. Simulation studies are conducted to assess the performance of the proposed methods. An application to smoking cessation data is reported to illustrate the use of the proposed methods. [ABSTRACT FROM AUTHOR]

The presence of measurement error is a widespread issue, which, when ignored, can render the results of an analysis unreliable. Numerous corrections for the effects of measurement error have been proposed and studied, often under the assumption of a normally distributed, additive measurement‐error model. In many situations, observed data are nonsymmetric, heavy‐tailed, or otherwise highly non‐normal. In these settings, correction techniques relying on the assumption of normality are undesirable. We propose an extension of simulation extrapolation that is nonparametric in the sense that no specific distributional assumptions are required on the error terms. The technique can be implemented when either validation data or replicate measurements are available, and is designed to be immediately accessible to those familiar with simulation extrapolation. [ABSTRACT FROM AUTHOR]

Measurement error and misclassification arise commonly in various data collection processes. It is well-known that ignoring these features in the data analysis usually leads to biased inference. With the generalized linear model setting, Yi et al. [Functional and structural methods with mixed measurement error and misclassification in covariates. J Am Stat Assoc. 2015;110:681–696] developed inference methods to adjust for the effects of measurement error in continuous covariates and misclassification in discrete covariates simultaneously for the scenario where validation data are available. The augmented simulation-extrapolation (SIMEX) approach they developed generalizes the usual SIMEX method which is only applicable to handle continuous error-prone covariates. To implement this method, we develop an R package, augSIMEX, for public use. Simulation studies are conducted to illustrate the use of the algorithm. This package is available at CRAN. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Though longitudinal data often contain missing responses and error-prone covariates, relatively little work has been available to simultaneously correct for the effects of response missingness and covariate measurement error on analysis of longitudinal data. Yi (2008) proposed a simulation based marginal method to adjust for the bias induced by measurement error in covariates as well as by missingness in response. The proposed method focuses on modeling the marginal mean and variance structures, and the missing at random mechanism is assumed. Furthermore, the distribution of covariates are left unspecified. These features make the proposed method applicable to a broad settings. In this paper, we develop an R package, called swgee, which implements the method proposed by Yi (2008). Moreover, our package includes additional implementation steps which extend the setting considered by Yi (2008). To describe the use of the package and its main features, we report simulation studies and analyses of a data set arising from the Framingham Heart Study. [ABSTRACT FROM AUTHOR]

It has been well documented that ignoring measurement error may result in severely biased inference results. In recent years, there has been limited but increasing research on causal inference with measurement error. In the presence of misclassified binary outcome variable, Shu and Yi (2017) considered the inverse probability weighted estimation of the average treatment effect and proposed valid estimation methods to correct for misclassification effects for various settings. To expedite the application of those methods for situations where misclassification in the binary outcome variable is a real concern, we implement correction methods proposed by Shu and Yi (2017) and develop an R package ipwErrorY for general users. Simulated datasets are used to illustrate the use of the developed package. [ABSTRACT FROM AUTHOR]

Inverse probability weighting (IPW) estimation has been widely used in causal inference. Its validity relies on the important condition that the variables are precisely measured. This condition, however, is often violated, which distorts the IPW method and thus yields biased results. In this paper, we study the IPW estimation of average treatment effects for settings with mismeasured covariates and misclassified outcomes. We develop estimation methods to correct for measurement error and misclassification effects simultaneously. Our discussion covers a broad scope of treatment models, including typically assumed logistic regression models and general treatment assignment mechanisms. Satisfactory performance of the proposed methods is demonstrated by extensive numerical studies. [ABSTRACT FROM AUTHOR]

Analysis of panel data is often challenged by the presence of heterogeneity and state misclassification. In this paper, we propose a hidden mover-stayer model to facilitate heterogeneity for a population that consists of two subpopulations each of movers or of stayers and to simultaneously account for state misclassification. We develop an inference procedure based on the expectation-maximization algorithm by treating the mover-stayer indicator and underlying true states as latent variables. We evaluate the performance of the proposed method and investigate the impact of ignoring misclassification through simulation studies. The proposed method is applied to analyze the data arising from the Waterloo Smoking Prevention Project. Copyright © 2017 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Generalized linear mixed models have been widely used in correlated data analysis. The applicability of these models is, however, hampered when data possess multilevel complex association structures. For instance, for longitudinal data arising in clusters, modelling complexity is a serious issue, and it is desirable to develop flexible models that are both computationally manageable and interpretatively meaningful. For these purposes, we propose a new class of flexible models, pairwise generalized linear mixed models, to facilitate correlated data that may possess multilevel complex association structures. Inferential procedures are developed to accommodate the proposed modelling framework, and asymptotic properties of the proposed method are established. The proposed models are evaluated through numerical studies. Copyright © 2017 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Missing observations in both responses and covariates arise frequently in longitudinal studies. When missing data are missing not at random, inferences under the likelihood framework often require joint modelling of response and covariate processes, as well as missing data processes associated with incompleteness of responses and covariates. Specification of these four joint distributions is a nontrivial issue from the perspectives of both modelling and computation. To get around this problem, we employ pairwise likelihood formulations, which avoid the specification of third or higher order association structures. In this paper, we consider three specific missing data mechanisms which lead to further simplified pairwise likelihood (SPL) formulations. Under these missing data mechanisms, inference methods based on SPL formulations are developed. The resultant estimators are consistent, and enjoy better robustness and computation convenience. The performance is evaluated empirically though simulation studies. Longitudinal data from the National Population Health Survey and Waterloo Smoking Prevention Project are analysed to illustrate the usage of our methods. [ABSTRACT FROM AUTHOR]

Covariate measurement error has attracted extensive interest in survival analysis. Since Prentice, a large number of inference methods have been developed to handle error-prone data that are modulated with proportional hazards models. In contrast to proportional hazards models, additive hazards models offer a flexible tool to delineate survival processes. However, there is little research on measurement error effects under additive hazards models. In this article, we systematically investigate this important problem. New insights into measurement error effects are revealed, as opposed to well-documented results for proportional hazards models. In particular, we explore asymptotic bias of ignoring measurement error in the analysis. To correct for the induced bias, we develop a class of functional correction methods for measurement error effects. The validity of the proposed methods is carefully examined, and we investigate issues of model checking and model misspecification. Theoretical results are established, and are complemented with numerical assessments. Supplementary materials for this article are available online. [ABSTRACT FROM PUBLISHER]

In contrast to extensive attention on model selection for cross-sectional data, research on model selection for longitudinal data remains largely unexplored. This is particularly the case when data are subject to missingness and measurement error. To address this important problem, we propose marginal methods that simultaneously carry out model selection and estimation for longitudinal data with missing responses and error-prone covariates. Our methods have several appealing features: the applicability is broad because the methods are developed for a unified framework with marginal generalized linear models; model assumptions are minimal in that no full distribution is required for the response process and the distribution of the true covariates is left unspecified; and the implementation is straightforward. To justify the proposed methods, we provide both theoretical properties and numerical assessments. [ABSTRACT FROM AUTHOR]

In survival analysis, covariate measurement error has been studied extensively for the Cox model. In this article, we propose a corrected profile likelihood approach, and show that many existing methods can be unified by our approach. Furthermore, we extend our discussion to general measurement error and Berkson models, as opposed to the classical additive error model that has been widely used in the literature. We investigate the impact of model misspecification of the measurement error process and uncover interesting findings. Empirical studies are carried out to illustrate the usage of the proposed methods and to assess their performance. The Canadian Journal of Statistics 43: 454-480; 2015 © 2015 Statistical Society of Canada [ABSTRACT FROM AUTHOR]

Covariate measurement imprecision or errors arise frequently in many areas. It is well known that ignoring such errors can substantially degrade the quality of inference or even yield erroneous results. Although in practice both covariates subject to measurement error and covariates subject to misclassification can occur, research attention in the literature has mainly focused on addressing either one of these problems separately. To fill this gap, we develop estimation and inference methods that accommodate both characteristics simultaneously. Specifically, we consider measurement error and misclassification in generalized linear models under the scenario that an external validation study is available, and systematically develop a number of effective functional and structural methods. Our methods can be applied to different situations to meet various objectives. [ABSTRACT FROM AUTHOR]

In longitudinal studies, missing observations occur commonly. It has been well known that biased results could be produced if missingness is not properly handled in the analysis. Authors have developed many methods with the focus on either incomplete response or missing covariate observations, but rarely on both. The complexity of modeling and computational difficulty would be the major challenges in handling missingness in both response and covariate variables. In this paper, we develop methods using the pairwise likelihood formulation to handle longitudinal binary data with missing observations present in both response and covariate variables. We propose a unified framework to accommodate various types of missing data patterns. We evaluate the performance of the methods empirically under a variety of circumstances. In particular, we investigate issues on efficiency and robustness. We analyze longitudinal data from the National Population Health Study with the use of our methods. Copyright © 2012 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Abstract: Many analyses for incomplete longitudinal data are directed to examining the impact of covariates on the marginal mean responses. We consider the setting in which longitudinal responses are collected from individuals nested within clusters. We discuss methods for assessing covariate effects on the mean and association parameters when covariates are incompletely observed. Weighted first and second order estimating equations are constructed to obtain consistent estimates of mean and association parameters when covariates are missing at random. Empirical studies demonstrate that estimators from the proposed method have negligible finite sample biases in moderate samples. An application to the National Alzheimer''s Coordinating Center (NACC) Uniform Data Set (UDS) demonstrates the utility of the proposed method. [Copyright &y& Elsevier]

Recurrent event data arise commonly in medical and public health studies. The analysis of such data has received extensive research attention and various methods have been developed in the literature. Depending on the focus of scientific interest, the methods may be broadly classified as intensity-based counting process methods, mean function-based estimating equation methods, and the analysis of times to events or times between events. These methods and models cover a wide variety of practical applications. However, there is a critical assumption underlying those methods-variables need to be correctly measured. Unfortunately, this assumption is frequently violated in practice. It is quite common that some covariates are subject to measurement error. It is well known that covariate measurement error can substantially distort inference results if it is not properly taken into account. In the literature, there has been extensive research concerning measurement error problems in various settings. However, with recurrent events, there is little discussion on this topic. It is the objective of this paper to address this important issue. In this paper, we develop inferential methods which account for measurement error in covariates for models with multiplicative intensity functions or rate functions. Both likelihood-based inference and robust inference based on estimating equations are discussed. The Canadian Journal of Statistics 40: 530-549; 2012 © 2012 Statistical Society of Canada [ABSTRACT FROM AUTHOR]

Covariate measurement error and missing responses are typical features in longitudinal data analysis. There has been extensive research on either covariate measurement error or missing responses, but relatively little work has been done to address both simultaneously. In this paper, we propose a simple method for the marginal analysis of longitudinal data with time-varying covariates, some of which are measured with error, while the response is subject to missingness. Our method has a number of appealing properties: assumptions on the model are minimal, with none needed about the distribution of the mismeasured covariate; implementation is straightforward and its applicability is broad. We provide both theoretical justification and numerical results. [ABSTRACT FROM PUBLISHER]

Misclassification is a longstanding concern in medical research. Although there has been much research concerning error-prone covariates, relatively little work has been directed to problems with response variables subject to error. In this paper we focus on misclassification in clustered or longitudinal outcomes. We propose marginal analysis methods to handle binary responses which are subject to misclassification. The proposed methods have several appealing features, including simultaneous inference for both marginal mean and association parameters, and they can handle misclassified responses for a number of practical scenarios, such as the case with a validation subsample or replicates. Furthermore, the proposed methods are robust to model misspecification in a sense that no full distributional assumptions are required. Numerical studies demonstrate satisfactory performance of the proposed methods under a variety of settings. [ABSTRACT FROM PUBLISHER]

The article discusses various reports published within the issue including one by Prentice and Huang on the association between nutrient intake and the risk of cancer, Qin and Zhang on the theory of optimal estimating functions in the context of length-biased sampling schemes and Yang and Nair on efficiency issues for semi-Markov multi-state processes under incomplete observation due to interval- and right-censoring.

Clustered longitudinal data feature cross-sectional associations within clusters, serial dependence within subjects, and associations between responses at different time points from different subjects within the same cluster. Generalized estimating equations are often used for inference with data of this sort since they do not require full specification of the response model. When data are incomplete, however, they require data to be missing completely at random unless inverse probability weights are introduced based on a model for the missing data process. The authors propose a robust approach for incomplete clustered longitudinal data using composite likelihood. Specifically, pairwise likelihood methods are described for conducting robust estimation with minimal model assumptions made. The authors also show that the resulting estimates remain valid for a wide variety of missing data problems including missing at random mechanisms and so in such cases there is no need to model the missing data process. In addition to describing the asymptotic properties of the resulting estimators, it is shown that the method performs well empirically through simulation studies for complete and incomplete data. Pairwise likelihood estimators are also compared with estimators obtained from inverse probability weighted alternating logistic regression. An application to data from the Waterloo Smoking Prevention Project is provided for illustration. The Canadian Journal of Statistics 39: 34-51; 2011 © 2010 Statistical Society of Canada [ABSTRACT FROM AUTHOR]

Abstract: Progressive multi-state models provide a convenient framework for characterizing chronic disease processes where the states represent the degree of damage resulting from the disease. Incomplete data often arise in studies of such processes, and standard methods of analysis can lead to biased parameter estimates when observation of data is response-dependent. This paper describes a joint analysis useful for fitting progressive multi-state models to data arising in longitudinal studies in such settings. Likelihood based methods are described and parameters are shown to be identifiable. An EM algorithm is described for parameter estimation, and variance estimation is carried out using the Louis’ method. Simulation studies demonstrate that the proposed method works well in practice under a variety of settings. An application to data from a smoking prevention study illustrates the utility of the method. [ABSTRACT FROM AUTHOR]

We describe methods for analyzing longitudinal binary data from cluster-randomized trials in which responses are incompletely observed and subjects may not be fully compliant with the prescribed treatment regimen. The method is based on a marginal regression model for the response where parameter estimates are obtained from generalized estimating equations. Estimating equations are also employed to estimate parameters of the missing data process which are used to compute inverse probability weights. A model is specified for the compliance process which facilitates estimating the expectation of the contributions to the estimating function for the response parameters among individuals without compliance data, which occurs when the control treatment involves no intervention. The approach isrobust in the sense that semi-parametric models are used for the response and the missing data processes and robust variance estimates are advocated. The proposed method is shown to perform well in simulation studies, and data from a randomized trial of patients with depression are analyzed for illustration. The Canadian Journal of Statistics 38: 232-255; 2010 © 2010 Statistical Society of Canada [ABSTRACT FROM AUTHOR]

Irreversible multi-state models provide a convenient framework for characterizing disease processes that arise when the states represent the degree of organ or tissue damage incurred by a progressive disease. In many settings, however, individuals are only observed at periodic clinic visits and so the precise times of the transitions are not observed. If the life history and observation processes are not independent, the observation process contains information about the life history process, and more importantly, likelihoods based on the disease process alone are invalid. With interval-censored failure time data, joint models are nonidentifiable and data analysts must rely on sensitivity analyses to assess the effect of the dependent observation times. This paper is concerned, however, with the analysis of data from progressive multi-state disease processes in which individuals are scheduled to be seen at periodic pre-scheduled assessment times. We cast the problem in the framework used for incomplete longitudinal data problems. Maximum likelihood estimation via an EM algorithm is advocated for parameter estimation. Simulation studies demonstrate that the proposed method works well under a variety of situations. Data from a cohort of patients with psoriatic arthritis are analyzed for illustration. Copyright © 2010 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]