Hello Tom, I will answer some of your questions below, Emmanuel and others may be better placed to reply to some of your questions:
On 12, Mar 2012, at 7:49 PM, Tom Schoenemann wrote: > Thanks Rob and Alejandro, > > OK, I did as suggested and ran a PGLS with A ~ B + C. I was hoping for some > clarification of the actual results. Here is a summary: > > ************************************************************** > Generalized least squares fit by maximum likelihood > Model: variableA ~ variableB + variableC > Data: DF.B.A.C > AIC BIC logLik > -23.49499 -10.46914 16.7475 > > Correlation Structure: corPagel > Formula: ~1 > Parameter estimate(s): > lambda > -0.09862731 > > Coefficients: > Value Std.Error t-value p-value > (Intercept) 0.5229794 0.04740728 11.031625 0.0000 > variableB 0.2200980 0.05012508 4.390976 0.0000 > variableC 0.0620030 0.05128472 1.208996 0.2296 > > Correlation: > (Intr) variableB > variableB -0.813 > variableC 0.362 -0.837 > > Standardized residuals: > Min Q1 Med Q3 Max > -3.2951355 -0.4995948 0.2604608 0.8884995 2.8456205 > > Residual standard error: 0.2067425 > Degrees of freedom: 100 total; 97 residual > ************************************************************** > > Are the following correct interpretations?: > > 1) Controlling for the phylogeny I used, variableB is associated with > variableA independent of variableC, because the p-value of the beta weight > for variableB is highly significant (0.0000) Yes, the model estimates a partial regression slope and standard error, that is the relationship between B and A controlling for the potential effects of C (that is potential relationship between C and A). > > 2) Controlling for the phylogeny I used, variableC is not significantly > associated with variableA independent of variableB, because the p-value of > its beta weight is not significant (0.2296) Yes, assuming there is no multicolinearity. See below... > > 3) There does not seem to be a significant effect of phylogeny on this > relationship, since the ML lambda estimate is: -0.09862731 Yes, when lambda tends to 0, phylogenetic and non phylogenetic methods are expected to converge. I will note that an advantage of using PGLS methods is that the evolutionary parameter estimated simultaneously with model fit (in this case lambda) allows for adequate adjustment for phylogenetic signal. See a nice paper on this by Revell 2010 in Methods in Ecology and Evolution. > > > Also, what exactly are the values listed in the "Correlation" section? Does > the -0.837 entry indicate that variableB is correlated negatively with > variableC controlling for variableA (and/or my phylogeny)? Maybe Emmanuel can answer this one. You could test whether B and C are strongly correlated, for example using PGLS. If they are repeating the analysis dropping B from your model should result in a significant correlation between C and A, indicating there is multicolinearity. Of course, the proper way to do all this is to examine your data prior to analyses. What are the two traits, maybe they are providing very similar information? > > > Regarding my original plan to assess the independent relationship between > variables using residuals, the Freckleton paper Alejandro kindly forwarded > includes this comment: > > "Note that to estimate the true slope for the effect of x2 using residual > regression one would need to regress the residuals of the regression on y on > x1 on the residuals of the regression of x2 on x1 (e.g. see Baltagi 1999, pp. > 7274 for elaboration of this)." (p. 544) > > This was what I remembered about the issue myself, though I haven't kept up > on the literature Rob and Alejandro mentioned. > > However, Rob believes the residuals might not be independent of phylogeny, > and that I should do a PGLS on them also. This leads to my next question: > what ARE the residuals of the PGLS then, if not also corrected for phylogeny? > In the case of my specific data, I see that the residuals from a PGLS of > variableA ~ variableB are not identical to the residuals of a simple lm of > variableA ~ variableB, so I assume that the phylogeny included in the PGLS is > having some effect on the residuals? Or is there another reason for the > difference? You can look at yet another paper by Revell(2009) on this issue. The issue is not so much whether traits present phylogenetic signal but rather whether the residuals of a linear model present phylogenetic signal, or more precisely whether there is covariance in the residuals because of phylogenetic relatedness. Hence, even if you extracted the residuals of different PGLS models you still control for phylogenetic non independence when analyzing the relationship between those residuals. Hope this helps! Alejandro > > Thanks for any clarifications! > > -Tom > > > On Mar 12, 2012, at 8:19 AM, Robert Barton wrote: > >> >> 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 > > > > On Mar 12, 2012, at 6:10 AM, Alejandro Gonzalez V wrote: > >> Hello, >> >> Why not simply use multiple regression ie A ~ B + C using gls and a >> correlation structure to control for phylogeny? Are you worried about >> multicolinearity? >> Use of residuals to control for the effects of a variable has been >> criticized, I include one paper on the issue by Rob Freckleton. >> >> Cheers >> >> Alejandro >> __________________________________ >> >> Alejandro Gonzalez Voyer >> Post-doc >> >> Estación Biológica de Doñana (CSIC) >> Avenida Américo Vespucio s/n >> 41092 Sevilla >> Spain >> >> Tel: +34- 954 466700, ext 1749 >> >> E-mail: alejandro.gonza...@ebd.csic.es >> >> Web-site (Under Construction): >> Group page: http://consevol.org/index.html >> Personal web-page: http://consevol.org/members/alejandro.html >> > _________________________________________________ > P. Thomas Schoenemann > > Associate Professor > Department of Anthropology > Indiana University > Bloomington, IN 47405 > Phone: 812-855-8800 > E-mail: t...@indiana.edu > > Open Research Scan Archive (ORSA) Co-Director > Consulting Scholar > Museum of Archaeology and Anthropology > University of Pennsylvania > > Homepage: http://mypage.iu.edu/~toms/ > > > > > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo __________________________________ Alejandro Gonzalez Voyer Post-doc Estación Biológica de Doñana Consejo Superior de Investigaciones Científicas (CSIC) Av Américo Vespucio s/n 41092 Sevilla Spain Tel: + 34 - 954 466700, ext 1749 E-mail: alejandro.gonza...@ebd.csic.es Web site (Under construction): Personal page: http://consevol.org/members/alejandro.html Group page: http://consevol.org/index.html For PDF copies of papers see: http://csic.academia.edu/AlejandroGonzalezVoyer [[alternative HTML version deleted]]
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