Hi Karin,
Thanks for the update. I can't get gls() to give an answer for the example data
using ML - I get this message:
Model1-gls(Trait1~Trait2,data=data,correlation=corPagel(1,tree,fixed=FALSE),method=ML)
Error in eigen(val) : infinite or missing values in 'x'
In addition: Warning message:
Hi Robin,
Please find below a function I wrote that does what you want. Let me
know if you have any questions, if you find any bugs or if you have
any suggestions to make it better.
Cheers,
-- François
##' Graft unsampled taxa onto a tree by simulating random trees.
##'
##' Based on a
Hi Robin (and others)
I am not sure what sorts of analyses you plan on doing but you might want
to look into some recent work by Helene Morlon and colleagues. She has
recently published two different approaches (2010 Plos Biology; 2011 PNAS)
to diversification rate which can fit birth-death (and
I could not have said it better myself!
Thanks, Luke!
Ted
From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on
behalf of Luke Matthews [lmatth...@activatenetworks.net]
Sent: Thursday, January 19, 2012 6:41 AM
To: r-sig-phylo@r-project.org
Subject: Re: [R-sig-phylo]
Hi,
I'm using the Picante package in R to calculate the Blomberg K. I'm
trying to test for a phylogenetic signal in my data. I'm using a
dataset with the PC score for 21 different species on a tree with
varying branch lengths. I did this using the code here:
Hello,
I am working on a project where I need to add annotation/comment data in
square brackets to my tree and export it in NEXUS format so it looks like
this:
0.9):0.6):0.6):0.8):0.5)*[!color=#-65536]*:1.3):0.7):1.0)
I need to do this so I can then import the tree into figtree and have the
Hi Daniel.
I can think of two possibilities:
1) This is an error.
2) Your tree has an extremely unusual shape (for instance, it has many
bifurcations very close to the present day).
On constant rate Yule trees, substituting 1s for the true branch lengths
does not (on average) bias K in any
