[phylocom-user] aot varcontr

Scott Chamberlain schamber at rice.edu
Sun Nov 15 10:46:15 PST 2009


I am confused about what varcontr is actually calculating in the aot or aotf

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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