Tuesday, July 15, 2014

This is from awhile ago--I found it in my drafts, but I just wanted to reopen this can of worms.
selecting priors:

1) select random node on the tree:
#randomly sample a node from a randomly trimmed tree
random.node<-sample(tree.trim$edge[1,], 1)
> random.node
[1] 75

2) open up mesquite and simulate random character in Brownian motion on the tree and look at before and after rates on node 75 in Mesquite using these instructions:

Take the rate at node 75 for sig1 1 prior: -0.86245
Pick random branch within this clade for sig2 prior (Pellorneum_pyrrogenys):1.1092
Alpha: random uniform distribution runif(1)
rand.shift = 0.05 --used what Revell, et al uses
use ngen=100,000

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