I am trying to correctly specify a nested phylogenetic model in brms where the nested random term needs to be constrained by the phylogeny. i.e. within my model I have the term +(1|Region/Species) and cov_ranef=list(Species = A) where A is the phylo structure (I followed the phylo brms vignette).
Where my concern arises is: if I run the phylogenetic signal hypothesis test I have to add in sd_Region:Species__Intercept etc for it to work on my nested structure but as I haven’t specified the nested structure in the cov_ranef argument I’m convinced I must be doing something wrong. I’ve tried inputting it as cov_ranef=list(Region:Species = A) but this doesn’t work.
Any help/advice would be much appreciated as I trying to carefully learn how to use Bayesian GLMM methods correctly.
Thanks in advance,
Please also provide the following information in addition to your question:
- Operating System: Windows 10
- brms Version: 2.3.1