Abstract
Recent advances in technology contribute to a fast-growing number of studies utilizing intensive longitudinal data, and call for more flexible methods to address the demands that come with them. One issue that arises from collecting longitudinal data from multiple units in time is nested data, where the variability observed in such data is a mixture of within-unit changes and between-unit differences. This article aims to provide a model-fitting approach that simultaneously models the within-unit changes with differential equation models and accounts for between-unit differences with mixed effects. This approach combines a variant of the Kalman filter, the continuous-discrete extended Kalman filter (CDEKF), and the Markov chain Monte Carlo method often employed in the Bayesian framework through the platform Stan. At the same time, it utilizes Stan's functionality of numerical solvers for the implementation of CDEKF. For an empirical illustration, we applied this method in the context of differential equation models to an empirical dataset to explore the physiological dynamics and co-regulation between couples.