Hi, I’m learning to do a Bayesian inference with normal-inverse-gamma conjugate prior.
array[n] real y;
real mu0 = 0;
real lambda = 0.054;
real alpha = 1.12;
real beta = 0.4;
sigma2 ~ inv_gamma(alpha, beta);
mu ~ normal(mu0, sqrt(sigma2) / sqrt(lambda));
y ~ normal(mu, sqrt(sigma2));
I’m seeing the following error but not sure why my statement is not a prior:
Building: found in cache, done.
Messages from stanc:
Warning: The parameter mu has no priors.
I’m using Python 3.9.10 and pystan 3.4.0, and the code works fine with 2.x pystan.
Also, if I replace sqrt(sigma2) with a number such as 2, it would run without issue. Is there something wrong with my code?
Weird. You definitely have a prior structure there, so seems like a parsing failure. I suggest you use cmdstanpy rather than PyStan as cmdstanpy will have the most up-to-date version of Stan & it’s parsing tools.
Edit: oh, I see now that you’re using PyStan 3.4, which is indeed using the newest Stan (2.29). Hm. Maybe try with cmdstanpy anyway and report back?
The source of the message is indeed pedantic mode, which PyStan turns on by default.
I still think turning on pedantic mode is a good idea. Pedantic mode plays to Stan’s strengths. It’s precisely the sort of thing you’d expect to see in Stan and not in, for instance, PyTorch or Tensorflow Probability.
That said, the warning is confusing. Could it be made more verbose or reduced to an “Info:” message? How about “Note: The parameter mu has not been given a prior distribution.”