Scott Chamberlain wrote:
In Felsenstein's 2008 AmNat paper he states Likelihood ratio rest
(LRT) are available of the hypotheis that a set of q characters
have on phylogenetic covariation with the remaining p - q
characters. And his software contrast gives only one LRT result in
the output even if you have say 3 traits. If you are interested in
contrasts and a LRT for all pairwise relationships of the 3 traits,
do you just run analyses 3 different times, each with the pair of
traits you are interested in?
You can do all three tests, but they are not
independent tests. In Contrast I allow the user to
specify two sets of characters and test whether
they have evolved independently.
If you want to do all three possible tests:
1 versus (2,3), 2 versus (1,3), and 3 versus (1,2)
keep in mind that those tests are not
independent tests (for example, a strong
correlation between 2 and 3 could cause
two of the tests to show nonindependence.
You would need to run Contrast three times
to do those tests.
Perhaps what is needed is a test that
finds the two sets to divide the characters
into, sets that are as much independent as
possible. I have no immediate ideas how.
J.F.
Joe Felsenstein, j...@gs.washington.edu
Dept. of Genome Sciences, Univ. of Washington
Box 355065, Seattle, WA 98195-5065 USA
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