You can try this:
tree<- compute.brtime(tree, tree$Nnode:1)
It will produce an ultrametric tree with its nodes well separated.
I hope it helps
All the best
--
Dr. Juan A. Balbuena
Cavanilles Institute of Biodiversity and Evolutionary Biology
Symbiont Ecology and Evolution Lab
University of
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
As an update to my question--when I try to calibrate the tree itself using the
default single root calibration and default 1/1 min/max ages, the function
appears to run fine. When I add in my calibration table, the function exits
with the -Inf LL.
The tree is rooted. There are no duplicated
I didn't see the email that this addresses, but I will add a couple of
comments to Juan's suggestion:
(1) phytools::cophylo does not require the input trees to have branch
lengths. If they do not, arbitrary branch lengths for plotting are
computed using ape::compute.brlen.
(2) The code
Danielle,
Apologies for the late comment on this, but what do you mean by non-rooted?
Do you mean the tree is rooted, but has a three-way split with the outgroup
at the root node? You shouldn't do OU on a tree you can't assign a root to.
I'm also just a bit curious what gave you the sense that