A colleague of mine has asked me for help. She has a large amount of patient data involving clinical psychological measures (e.g., questions related to specific symptoms) gathered both before and after a psychological intervention in the same subjects. She believes there to be latent states within these data – representing different phases of the disorder (during the initial or final time point) or recovery (during the final time point). She is interested in applying a statistical model capable of taking data from 9 observed variables (representing answers to questions on a 4-point ordinal scale), each measured in ~2000 participants, and estimating the latent state for each participant at time one and at time two, and further estimating the transition probabilities between states from pre-measurement to post-measurement.
Being relatively new to this form of analysis, I am unsure how best to proceed. This sounds to me like some variant of a latent transition analysis, but I have been unable to find any examples showing how such an analysis could be implemented in any free analysis framework (e.g., R, Python). I would be most appreciative if someone could point me in the right direction.