Dear Tom, There is no reason to assume that the residuals from your two PGLS analyses will be independent of phylogeny, so if you are going to do this you should correlate the residuals phylogenetically (i.e. run them through PGLS). General problems with using residuals as data have been commented on in the literature by people like Freckleton, but I think that in the situation where each variable of interest is regressed on the same confounding variable it is valid to use residuals - because the correlation between the residuals is the same as the partial correlation between them. However, the simplest solution for this analysis would be to regress A on B and C in a single PGLS.
Rob Barton On 12/03/2012 11:00, "r-sig-phylo-requ...@r-project.org" <r-sig-phylo-requ...@r-project.org> wrote: > 3. partial correlation with gls residuals? (Tom Schoenemann) Hello, I was hoping to get some feedback on whether I'm doing something legitimate. Basically, I have 3 variables (say: A, B, and C) measured on 100 species, and I want to see whether A and B correlate with each other after controlling for C, and for phylogeny at the same time. Here is what I thought seems reasonable: 1) do a gls with variable A predicted by variable C, using a corPagel correlations structure derived from a phylogeny of these species to control for phylogenetic effects. The residuals from this are then extracted 2) do a gls with variable B predicted by variable C, using the same method, also extracting the residuals for this comparison 3) do a simple lm of the residuals from step 1 vs. the residuals from step 2 I guess my question is, are the residuals from the gls independent of my phylogeny? If they are, then wouldn't this give me the partial correlation between A and B, controlling for C, and for phylogeny? Or is there a better (or alternative) way to do this? Thanks for any suggestions, -Tom --------------------------------------------------------- Professor Robert Barton Professor of Evolutionary Anthropology President, European Human Behaviour & Evolution Association email: r.a.bar...@durham.ac.uk Address: Department of Anthropology, Durham University, Dawson Building, South Road, Durham, DH1 3LE U.K. Tel. +44 (0)191 334 1603 Mobile +44 (0)7507564773 RAI's First Annual Postgraduate Conference at Durham 2011: http://www.dur.ac.uk/rai.postgrad/ <http://www.dur.ac.uk/rai.postgrad/> Department: http://www.dur.ac.uk/anthropology/ Evolutionary Anthropology Research Group: http://www.dur.ac.uk/anthropology/research/earg/ Phylogeny of Sleep project: http://www.bu.edu/phylogeny/ Evolutionary Architecture of Reproduction project: http://www.dur.ac.uk/reproductionproject/ European Human Behaviour & Evolution Association: http://www.ehbea.com/ _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo