To analyze longitudinal zero-inflated count data, we extend existing models by introducing marginalized zero-inflated Poisson (MZIP) models with random effects, which explicitly capture the marginal effect of covariates and address limitations of previous methods. These models provide a clearer interpretation of the overall mean effect of covariates on zero-inflated count data. To further accommodate overdispersion, we develop marginalized zero-inflated negative binomial (MZINB) models. Both models incorporate subject-specific heterogeneity through a flexible random effects covariance structure. Simulation studies are conducted to evaluate the performance of the MZIP and MZINB models, comparing their inference under both homogeneous and heterogeneous random effects. Finally, we illustrate the applicability of the proposed models through an analysis of systemic lupus erythematosus data.

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