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davharris / mistnet

stochastic neural networks in R
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Building phylogenetic covariance matrices #95

Open davharris opened 10 years ago

davharris commented 10 years ago

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 commented 10 years ago

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

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