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July 28, 2014
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MODELING WITH MISSING DATA

Mplus has several options for the estimation of models with missing data. Mplus provides maximum likelihood estimation under MCAR (missing completely at random), MAR (missing at random), and NMAR (not missing at random) for continuous, censored, binary, ordered categorical (ordinal), unordered categorical (nominal), counts, or combinations of these variable types (Little & Rubin, 2002). MAR means that missingness can be a function of observed covariates and observed outcomes. For censored and categorical outcomes using weighted least squares estimation, missingness is allowed to be a function of the observed covariates but not the observed outcomes. When there are no covariates in the model, this is analogous to pairwise present analysis. Non-ignorable missing data (NMAR) modeling is possible using maximum likelihood estimation where categorical outcomes are indicators of missingness and where missingness can be predicted by continuous and categorical latent variables (Muthén, Jo, & Brown, 2003; Muthén et al., 2010 ).

In all models, missingness is not allowed for the observed covariates because they are not part of the model. The model is estimated conditional on the covariates and no distributional assumptions are made about the covariates. Covariate missingness can be modeled if the covariates are brought into the model and distributional assumptions such as normality are made about them. With missing data, the standard errors for the parameter estimates are computed using the observed information matrix (Kenward & Molenberghs, 1998). Bootstrap standard errors and confidence intervals are also available with missing data.

Mplus provides multiple imputation of missing data using Bayesian analysis (Rubin, 1987; Schafer, 1997). Both the unrestricted H1 model and a restricted H0 model can be used for imputation.

Multiple data sets generated using multiple imputation can be analyzed using a special feature of Mplus. Parameter estimates are averaged over the set of analyses, and standard errors are computed using the average of the standard errors over the set of analyses and the between analysis parameter estimate variation (Rubin, 1987; Schafer, 1997). A chi-square test of overall model fit is provided (Asparouhov & Muthén, 2008c; Enders, 2010).

Modeling with Complex Survey Data Estimators and Algorithms
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