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,
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http://www.dur.ac.uk/anthropology/research/earg/
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