I recommend looking at chapter 6 of Paul Allison's *Fixed Effects
Regression Models*.  This chapter outlines how you can use a structural
equation modeling framework to estimate a multi-level model (a random
effects model).  This approach is slower than just using MLM software like
lmer() in the lme4 package, but has the advantage of being able to specify
correlations between errors across time, the ability to control for
time-invariant effects of time-invariant variables, and allows you to use
the missing data maximum likelihood that comes in structural equation
modeling packages.

Andrew Miles

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