Hello, So what you're suggesting is that I do that and then fit<-gls(X~Y,corr=corBrownian(1,t.pb),data=df,method="ML", right?
Thanks. Best regards, Sérgio. ᐧ 2015-04-13 18:42 GMT+01:00 Liam J. Revell <[email protected]>: > Hi all. > > I just wanted to add that it should be straightforward to sample edge > lengths as if they arose under a specific process. For instance, here on my > blog I show how to sample branching times & edge lengths as if they arose > under a pure-birth (i.e., 'Yule') process, given a particular input > topology: http://blog.phytools.org/2015/04/sampling-edge-lengths- > under-yule-process.html. For things like the phylogenetic (contrasts) > regression, this may be preferable to Grafen's edge lengths, which tend to > make recent edge lengths very short, giving very high weight to the > associated contrasts. > > All the best, Liam > > Liam J. Revell, Assistant Professor of Biology > University of Massachusetts Boston > web: http://faculty.umb.edu/liam.revell/ > email: [email protected] > blog: http://blog.phytools.org > > > On 4/13/2015 1:13 PM, Sergio Ferreira Cardoso wrote: > >> 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]/
