Dear all, I'm analysing a small data set consisting of values for 27 taxa. I am extracting phylogenetic residuals from a regression (as in Revell, 2009) to be used as size corrected values. Almost all the residuals are negative because the regression line is positioned above what I would expect. Do you think this has something to do with the phylogeny? It probably has because everything looks fine with the ordinary least-squares. Thanks in advance.
All the best, Sérgio. Here is the coding I used: ## Used packages > library("ape", lib.loc="~/R/win-library/3.1") > library("caper", lib.loc="~/R/win-library/3.1") > library("nlme", lib.loc="~/R/win-library/3.1") > library("phytools", lib.loc="~/R/win-library/3.1") > library("phangorn", lib.loc="~/R/win-library/3.1") ## fitting PGLS > fit_brain<-pgls(perimeter~brain,comparative.data(tree,df,"Species")) > summary(fit_brain) ## cross checking using phytools > phyl.resid(tree,brain,perimeter,method="BM") ## quick plotting > plot(brain,perimeter) > abline(fit_brain) > ols<-lm(perimeter~brain,data=df) > abline(ols) -- Com os melhores cumprimentos, Sérgio Ferreira Cardoso. -------------------- Best regards, Sérgio Ferreira Cardoso MSc. Paleontology candidate Departamento de Ciências da Terra - FCT /Universidade Nova de Lisboa Geociências - Universidade de Évora Lisboa, Portugal [[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/