Than you all.
Best regards, Sérgio. ᐧ 2015-04-13 22:02 GMT+01:00 Emmanuel Paradis <[email protected]>: > Le 13/04/2015 19:13, Sergio Ferreira Cardoso a écrit : > >> Hello, >> >> Thank you both for the help. >> Emmanuel, so is there a way to see contrasts in R? >> > > Yes! The function pic() has been in ape since its first release (ver. 0.1 > in Aug 2002), and there is an option to output the contrasts scaled or not. > > best, > > Emmanuel > > 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] >> <mailto:[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 >> > > -- 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]/
