[phylocom-user] aot varcontr

Steven Kembel steve.kembel at gmail.com
Sun Nov 15 11:09:27 PST 2009

Hi Scott,

VarContr in the aot/aotf output is the observed variance of  
standardized contrasts.

The observed variance of standardized contrasts is calculated as  
sum(squared standardized contrast values)/(N-1), as described by  
Blomberg and Garland.

VarCn.rankLow and VarCn.rankHi are the rank of the observed VarContr  
versus the distribution of randomized standardized contrasts. These  
can be used to calculate a P-value testing for phylogenetic signal in  
the traits. VarCn.rankLow divided by number of runs plus one is a one- 
tailed P-value testing for greater phylogenetic signal than expected.


On Nov 15, 2009, at 10:46 AM, Scott Chamberlain wrote:

> Hello,
> I am confused about what varcontr is actually calculating in the aot  
> or aotf output.
> Is the varcontr in the aot and aotr output the expected from the  
> randomizations, or the observed? I have been taking this as the  
> expected value from randomizations.
> In the phylocom manual, varcontr is described as the variance of  
> standardized contrasts across the tree. However, calculating the  
> observed variance of standardized contrasts is very far from the  
> expected varcontr, whereas variance of raw contrasts is closer to  
> the expected varcontr. Is the varcontr from the output actually the  
> variance of raw contrasts, not standardized contrasts?
> Thanks, Scott Chamberlain
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> phylocom-user mailing list
> phylocom-user at lists.phylodiversity.net
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