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Hidden Markov chains in generalized linear models

We show how the concept of hidden Markov model may be accommodated in a setting involving multiple sequences of observations. The resulting class of models allows for both interrelationships between different sequences and serial dependence within sequences. Missing values in the observation sequences may be handled in a straightforward manner. We also examine a group of methods, based upon the observed Fisher Information matrix, for estimating the covariance matrix of the parameter estimates. We illustrate the methods with both real and simulated data sets.