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Understanding student achievement over time is a primary focus of educational research. However, current practices in estimating student achievement over time often ignore complex nesting structures present in education data. For example, the multiple classrooms that students are members of over time. The current study seeks to provide guidance on applying a model demonstrated by Leroux and Beretvas (2018a) to estimate the variance associated with multiple classroom memberships over multiple years and to compare the effect of modeling classrooms on student variance and fixed effects when compared to a model that only estimates school level memberships.