Songbird on paired samples

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In my example I have subject ids directly coded : Show how to fit a random effects models with negative binomial · GitHub

This would require a small update to the input to the stan model highlighted in the above tutorial via

dat = {
    'N' : X.shape[0],
    'D' : table.shape[0],
    'p' : X.shape[1],
    'depth' : np.log(table.sum(axis='sample').values),
    'x' : X.values,
    'y' : table.values.astype(np.int64)
    'subj_ids' : <something goes here>
}

where subj_ids is some numeric conversion of your actual host subject ids.

There are also quite a bit of documentation on stan that I recommend checking out : Stan User’s Guide.

Also stan has its own channel ; for instance this page highlights an example fitting mixed effects models : Linear mixed effects model with varying intercept and slope in matrix notation - #3 by Wade - Modeling - The Stan Forums