Hello, Thank you both for the help. Emmanuel, so is there a way to see contrasts in R? Reading this paper - Garland, T., Harvey, P. H., & Ives, A. R. (1992). Procedures for the analysis of comparative data using phylogenetically independent contrasts. Systematic Biology, 41(1), 18-32. - I was aware of the importance of standardizing contrasts and of comparing Absolute value of standard contrat vs Standard deviation of contrast. I've learned to do this in Mesquite but I don't know if R alows this to be done. When I run the GLS I ask R to estimate the rho, so, a priori I never know the rho value.
Maybe I'm really really confused, but here is the reason why I tthink something isn't right with my analysis: I built a phylogenetic tree in Mesquite, and based on several works I used million years as branch lengths. It makes sense for me because I'll be using a fossil on my analysis. But I tested the tree before adding the extinct taxa, so to make sure everything was OK when the tree was ultrametric. I noticed that, for example, whatever the independent variable (X) was, the alpha from OU was extremely high (0.999182, for instance). It would always be 0.999. I thought maybe I was using the wrong transformation... That's why I ended up trying to know if I needed to do something prior to transforming and analysing the tree. Thank you very much. Best regards, Sérgio. ᐧ 2015-04-13 17:17 GMT+01:00 Emmanuel Paradis <[email protected]>: > Hi Sérgio, > > There is indeed generally a relationship between branch length > transformations and correlation structures. You may check that with the > function vcv2phylo, e.g.: > > > tr <- rcoal(20) > > co <- corGrafen(1, phy = tr) > > ts <- vcv2phylo(vcv(co)) > > all.equal(tr, ts) > [1] FALSE > > all.equal(compute.brlen(tr), ts) > [1] TRUE > > compute.brlen() transforms the branch lengths according to Grafen's model > with parameter rho = 1 (by default). Some other transformations of branch > lengths are available in package geiger. > > Best, > > Emmanuel > > Le 12/04/2015 21:47, Sergio Ferreira Cardoso a écrit : > >> Hi everyone, >> >> I'm relatively new in phylogenetic comparative methods. I'm a little >> confused about branch length transformations. I'm using a tree with >> divergence time (My) as branch lengths. When I use corPagel, corGrafen or >> corMartins in R, the branch lengths, are the branch lengths automatically >> transformed? e.g., gr.mammals<-corGrafen(1,phylo,fixed=F); >> fit<-gls(FCL~logBodymass,correlation=gr.mammals,data=df,method="ML"). >> My question may sound a bit nonsense but I've seen in some papers (e.g., >> Spoor, >> F., Garland, T., Krovitz, G., Ryan, T. M., Silcox, M. T., & Walker, A. >> (2007). The primate semicircular canal system and locomotion. *Proceedings >> of the National Academy of Sciences*, *104*(26), 10808-10812.) the >> indication that a PGLS was made without branch transformation, but no >> reference is made to the model (maybe it's corBrownian). >> >> Thank you very much. >> >> Best regards, >> Sérgio. >> >> > -- 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 - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
