I'm trying to use chronos (ape version 5.2) to scale a tree of ~800 tips, with
branch lengths derived from a RAxML analysis. I'm using 4 outgroup
calibrations. When I run the analysis using
t.og <- chronos(tree, lambda = 1, model = "relaxed", quiet = FALSE,
calibration = dd.out)
I
nodes with conflicting ages, and R
does not give errors about the formatting of the calibration table.
~John
From: R-sig-phylo on behalf of John S
Denton
Sent: Wednesday, December 12, 2018 1:20:20 PM
To: r-sig-phylo@r-project.org
Subject: [R-sig-phylo] ape
I'm trying to simulate different degrees of morphospace packing of geometric
morphometric coordinates ("packing" defined, for the purposes of this
exploration, as closely-abutting regions having minimal overlap with other
species in the space), using a tree and an empirical input covariance