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 _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
