General

• Vermunt and Hagenaars
• Neal

Autoregressive with Random Effects

• Mandel and Betensky including inference for a derived outcome that requires a condition to be met on two successive visits
• https://academic.oup.com/biostatistics/article/11/1/127/226327 includes latent variables
• Varin and Czado

Random Effects with Multistate

• Kim dissertation

Multistate Transition Models

• Noorian and Ganjali - Bayesian; see also here
• de Lara et al
• Lee and Daniels

Finite Mixture model

• Pennoni and Romeo

Multivariate Probit

• Chaubert, Mortier, Andre

Multilevel Model

• Dessie et al

Contrasting Marginal and Conditional Approaches

• da Silva, Amorim, Colosimo, Heller and here