How to Conduct Dynamic Multilevel Analysis using R?

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I'm currently conducting a study involving sequential analysis of dyadic data, in which actor's goals at Time 1 predict partner's goals at time 2. I have four types of categorical goal outcomes (self goal, partner goal, task goal, and relationship. At 'a new method for analyzing sequential data - dynamic multilevel analysis', Chiu and Khoo provides a great conceptual overview of the approach, but does not give any guidance on practical steps for conducting the analysis.
Reference:
Chiu, M. M., & Khoo, L. (2005). A new method for analyzing sequential processes: dynamic multilevel analysis. Small Group Research, 36(5), 600-631.
http://gse.buffalo.edu/fas/chiu/pdf/New_Method_for_Analyzing.pdf
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