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 particular direction.
If you share your tree and data I would be happy to look at the issue
more closely.
All the best, Liam
--
Liam J. Revell
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://phytools.blogspot.com
On 1/19/2012 9:53 PM, dwe...@life.illinois.edu wrote:
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:
http://bodegaphylo.wikispot.org/IV._Testing_Phylogenetic_Signal_in_R
I got a K statistic of 0.0006457603 and yet the resultant PIC.variance.P
is 0.001. If I'm correct, the PIC.variance.P is the p-value and
significant at 0.05. Is that correct?
I then decided to play with my data and set all branch lengths equal to
1 to see how that would affect things. I got a K statistic of 2.921763
and a PIC.variance.P value of 0.001. My understanding is that K
statistics close to 0 are not significant and become significant close
to and above 1.
I'm confused why I got a significant p-value for both K statistics, even
though one is very close to 0 (0.00065) and the other is above 2. I
would appreciate any help in explaining Picante and the K statistic.
Thank you.
-Daniel
----><((((º> -----><((((º> ----><((((º> ----><((((º> ----><((((º> ----
Daniel P Welsh
PhD Candidate
Teaching Assistant
Department of Animal Biology
University of Illinois at Urbana-Champaign
202 Shelford Vivarium
606 E. Healey Street
Champaign, IL 61821
lab phone: (217) 333-5323
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