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Background

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.

Question

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.

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Your colleague can apply a latent class analysis through which a latent variable relying on the clinical psychological measures can be identified. You may refer to the poLCA package by Lenzer and Lewis in R:

https://cran.r-project.org/web/packages/sBIC/vignettes/LatentClassAnalysis.pdf

For the longitudinal analysis between point 1 and point 2, you may refer to the Latent Class Growth Analysis

Extensive details are provided by Feldman et al.:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2791967/

In R, you may refer to this relatively new package by Proust-Lima et al.:

https://cran.r-project.org/web/packages/lcmm/lcmm.pdf

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