I’m trying to specify a hierarchical multivariate probit model based off the example in the manual. I’m having some problems. Initially, I was also including (strongly regularised) group level covariates, but the model wouldn’t at all initialise, so I took them out and tried to work out what the minimal model I could get to run was, as per other advice I’ve seen on this forum. I’m initialising values generated from from univariate runs of the same dataset. The model now runs, with the standard Jacobian warning, but I’m 90% sure that I’m not doing any non-linear transformations of the variables. But it’s mixing --terribly-- (the log posterior doesn’t seem to be getting near convergence at all), and I’m getting a low BFMI.
I was wondering if anyone would be willing to point me in the right direction towards spotting what the issue is here so I can have a go at fixing it, then hopefully I can add the group level covariates back in and break it all over again!
Model, data, traceplot and R code attached. Apologies for the messiness of the code, I’m pretty new to stan coding. (I could only put a single attachment up, so here’s everything in a dropbox link https://www.dropbox.com/sh/7f63of1r3nrshw9/AAC0co2lY_At75_qQZ9UEwwQa?dl=0)