[R-sig-phylo] Blomberg K Statistic

Liam J. Revell liamjrevell at gmail.com
Fri Jan 20 05:06:42 CET 2012

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.revell at umb.edu
blog: http://phytools.blogspot.com

On 1/19/2012 9:53 PM, dwelsh at 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
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