Building phylogenetic covariance matrices

[davharris]

I think this is all I need to do:

# Covariance matrix under an OU model
base.covar = vcv(rescale(tre2, sigsq = 1, alpha = 0.1, model = "OU"))
# Add squared standard error to the diagonal
covar = base.covar + SE^2 * diag(length(tre2$tip.label))

[davharris]

I think I can get all of the parameter estimates for the above with

fitContinuous(phy = phylo, dat = latent.trait, model = "OU", SE = NA)