A common challenge in developmental research is the amount of incomplete and missing data that occurs from respondents failing to complete tasks or questionnaires, as well as from disengaging from the study (i.e., attrition). This missingness can lead to biases in parameter estimates and, hence, in the interpretation of findings. These biases can be addressed through statistical techniques that adjust for missing data, such as multiple imputation. Although multiple imputation is highly effective, it has not been widely adopted by developmental scientists given barriers such as lack of training or misconceptions about imputation methods. Utilizing default methods within statistical software programs like listwise deletion is common but may introduce additional bias. This manuscript is intended to provide practical guidelines for developmental researchers to follow when examining their data for missingness, making decisions about how to handle that missingness and reporting the extent of missing data biases and specific multiple imputation procedures in publications.
more »
« less
dynr.mi: An R Program for Multiple Imputation in Dynamic Modeling
Assessing several individuals intensively over time yields intensive longitudinal data (ILD). Even though ILD provide rich information, they also bring other data analytic challenges. One of these is the increased occurrence of missingness with increased study length, possibly under non-ignorable missingness scenarios. Multiple imputation (MI) handles missing data by creating several imputed data sets, and pooling the estimation results across imputed data sets to yield final estimates for inferential purposes. In this article, we introduce dynr.mi(), a function in the R package, Dynamic Modeling in R (dynr). The package dynr provides a suite of fast and accessible functions for estimating and visualizing the results from fitting linear and nonlinear dynamic systems models in discrete as well as continuous time. By integrating the estimation functions in dynr and the MI procedures available from the R package, Multivariate Imputation by Chained Equations (MICE), the dynr.mi() routine is designed to handle possibly non-ignorable missingness in the dependent variables and/or covariates in a user-specified dynamic systems model via MI, with convergence diagnostic check. We utilized dynr.mi() to examine, in the context of a vector autoregressive model, the relationships among individuals’ ambulatory physiological measures, and self-report affect valence and arousal. The results from MI were compared to those from listwise deletion of entries with missingness in the covariates. When we determined the number of iterations based on the convergence diagnostics available from dynr.mi(), differences in the statistical significance of the covariate parameters were observed between the listwise deletion and MI approaches. These results underscore the importance of considering diagnostic information in the implementation of MI procedures.
more »
« less
- Award ID(s):
- 1806874
- PAR ID:
- 10101179
- Date Published:
- Journal Name:
- World academy of science, engineering and technology
- Volume:
- 13
- Issue:
- 5
- ISSN:
- 1307-6892
- Page Range / eLocation ID:
- 302 - 311
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
We consider quantile estimation in a semi-supervised setting, characterized by two available data sets: (i) a small or moderate sized labeled data set containing observations for a response and a set of possibly high dimensional covariates, and (ii) a much larger unlabeled data set where only the covariates are observed. We propose a family of semi-supervised estimators for the response quantile(s) based on the two data sets, to improve the estimation accuracy compared to the supervised estimator, i.e., the sample quantile from the labeled data. These estimators use a flexible imputation strategy applied to the estimating equation along with a debiasing step that allows for full robustness against misspecification of the imputation model. Further, a one-step update strategy is adopted to enable easy implementation of our method and handle the complexity from the non-linear nature of the quantile estimating equation. Under mild assumptions, our estimators are fully robust to the choice of the nuisance imputation model, in the sense of always maintaining root-n consistency and asymptotic normality, while having improved efficiency relative to the supervised estimator. They also attain semi-parametric optimality if the relation between the response and the covariates is correctly specified via the imputation model. As an illustration of estimating the nuisance imputation function, we consider kernel smoothing type estimators on lower dimensional and possibly estimated transformations of the high dimensional covariates, and we establish novel results on their uniform convergence rates in high dimensions, involving responses indexed by a function class and usage of dimension reduction techniques. These results may be of independent interest. Numerical results on both simulated and real data confirm our semi-supervised approach's improved performance, in terms of both estimation and inference.more » « less
-
Abstract Biobanks that collect deep phenotypic and genomic data across many individuals have emerged as a key resource in human genetics. However, phenotypes in biobanks are often missing across many individuals, limiting their utility. We propose AutoComplete, a deep learning-based imputation method to impute or ‘fill-in’ missing phenotypes in population-scale biobank datasets. When applied to collections of phenotypes measured across ~300,000 individuals from the UK Biobank, AutoComplete substantially improved imputation accuracy over existing methods. On three traits with notable amounts of missingness, we show that AutoComplete yields imputed phenotypes that are genetically similar to the originally observed phenotypes while increasing the effective sample size by about twofold on average. Further, genome-wide association analyses on the resulting imputed phenotypes led to a substantial increase in the number of associated loci. Our results demonstrate the utility of deep learning-based phenotype imputation to increase power for genetic discoveries in existing biobank datasets.more » « less
-
This study compares two missing data procedures in the context of ordinal factor analysis models: pairwise deletion (PD; the default setting in Mplus) and multiple imputation (MI). We examine which procedure demonstrates parameter estimates and model fit indices closer to those of complete data. The performance of PD and MI are compared under a wide range of conditions, including number of response categories, sample size, percent of missingness, and degree of model misfit. Results indicate that both PD and MI yield parameter estimates similar to those from analysis of complete data under conditions where the data are missing completely at random (MCAR). When the data are missing at random (MAR), PD parameter estimates are shown to be severely biased across parameter combinations in the study. When the percentage of missingness is less than 50%, MI yields parameter estimates that are similar to results from complete data. However, the fit indices (i.e., χ2, RMSEA, and WRMR) yield estimates that suggested a worse fit than results observed in complete data. We recommend that applied researchers use MI when fitting ordinal factor models with missing data. We further recommend interpreting model fit based on the TLI and CFI incremental fit indices.more » « less
-
Abstract This manuscript extends the definition of the Absolute Standardized Mean Difference (ASMD) for binary exposure (M = 2) to cases for M > 2 on multiple imputed data sets. The Maximal Maximized Standardized Difference (MMSD) and the Maximal Averaged Standardized Difference (MASD) were proposed. For different percentages, missing data were introduced in covariates in the simulated data based on the missing at random (MAR) assumption. We then investigate the performance of these two metric definitions using simulated data of full and imputed data sets. The performance of the MASD and the MMSD were validated by relating the balance metrics to estimation bias. The results show that there is an association between the balance metrics and bias. The proposed balance diagnostics seem therefore appropriate to assess balance for the generalized propensity score (GPS) under multiple imputation.more » « less
An official website of the United States government

