Running R v. 3.6.0, rstan v. 2.19.3, brms v. 2.13.0 on Ubuntu 18.04.2 LTS.
I’m trying to run a relatively simple phylogenetic regression for some COVID work (I’m afraid it involves confidential patient data, so I can’t share it). Normally I’d just code this up in a full Stan model, but seeing as it was simple, I thought I’d give brms a go.
I’m getting an error when I try to run it (in the test case of the minimal model with just the intercept and the phylogenetic random effect):
Error: Within-group covariance matrices must be positive definite.
Now phylogenetic covariance matricies are only guarenteed to be positive semi-definite (and this one is positive semi-definite not positive definite), I was wondering, is the positive definite condition required for some computational reason I’m missing, or is this just a case of the test being applied being overly strict?