Also worth noting is that people often use taxonomic levels if they don't have a tree. Trees are more available than might be expected (though still far less available than they should be), so you can get a tree and use phylogenetic comparative methods.
Sources of trees: https://tree.opentreeoflife.org/ https://www.treebase.org/ https://phylo.cs.nmsu.edu/ http://datelife.org/ (though the datelife R package <https://github.com/phylotastic/datelife> may be more useful, depending on scale) https://datadryad.org/ Plus people make individual trees available: large trees for birds, sharks and rays, plants, etc. that may not be deposited into a formal repository but are on a website, plus trees stored as supplemental info in papers. So if you're using taxonomy as a predictor because there doesn't seem to be a good tree, there might actually be one with a bit of digging. Best, Brian _______________________________________________________________________ Brian O'Meara, http://brianomeara.info, especially Calendar <http://brianomeara.info/calendar.html>, CV <http://brianomeara.info/cv.html>, and Feedback <http://brianomeara.info/feedback.html> Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville He/Him/His On Wed, Sep 11, 2019 at 1:33 AM Joe Felsenstein <j...@gs.washington.edu> wrote: > Oscar Inostraza -- > > Is the variable x also evolving on the tree? If so you need to use > standard phylogenetically-informed comparative methods to estimate the > variances and covariances of changes in both characters. > > You may not be able to assume that y responds instantly to x. > > J.F. > ---- > Joe Felsenstein, j...@gs.washington.edu > Department of Genome Sciences, University of Washington, Box 355065, > Seattle, WA. 98195-5065 USA > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
