Hi all, I’ve been fiddling with phylogenetic mixed models from evolutionary biology recently. In these models, you have a “random” effect featuring a VCV (derived from an estimated phylogeny) that’s known up to a constant. They’re mechanically identical to animal models (of which Diogo Melo has a S…

You can code this model in Stan and it should proably work a lot better than trying to sample the K. Here’s the BUGS: Y[1:Nspec] ~ dmnorm(mu[],TAU[,]) ... K ~ dcat(p[]) for (i in 1:Nspec) { for (j in 1:Nspec) { TAU[i,j] <- tau*invA[i,j,K] } } Here’s what you’d do in Stan to marginalize ou…

Sampling over an uncertain variance covariance matrix

Modeling

Charles_Driver February 8, 2018, 1:07pm 2

I recently posted an approach I have used here: Non-static covariance matrices?

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Sampling over an uncertain variance covariance matrix

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