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?

Topic		Replies	Views
Including Phylogenetic Information in a Bayesian Hierarchical Model for Predicting Species Trait Modeling cmdstan , rstan , brms	1	51	September 19, 2024
Prior on real<lower=0,upper=1> with half mass in 0 Modeling priors	4	517	April 30, 2020
Implementing phylogenetic logistic regression for binary response variable in Stan Modeling techniques , specification	5	1185	March 27, 2019
Mixture model with unknown k Modeling	7	1438	November 14, 2017
Model averaged parameter estimates Modeling loo	3	988	February 9, 2018

Sampling over an uncertain variance covariance matrix

Related topics