Hi Emma, Thank you. My co-worker calculated the nodes, MorphoJ does not seem to provide that info but some papers do mention they used it for that end (if I am not wrong).
By the way, we obtained a K=0.54 and P=0.001. If I understand it correctly, that indicates that there is substantial convergence in the data, and that pattern observed isn't random. Does that mean then that the phylogenetic signal is week? Or am I interpreting things the wrong way. In MorphoJ I obtain a significant phylogenetic signal. Thanks Filipe 2016-05-20 8:43 GMT+03:00 Emma Sherratt <emma.sherr...@gmail.com>: > Hi Filipe, > > I believe you cannot directly. When you use the "Map onto phylogeny" > option in MorphoJ, you will have appear in the scene tree the tree icon, > and two dataset icons below that. "BranchDiffs" and "IndContrasts". From > the MorphoJ helpGuide: > *Each analysis produces two output data sets: one with the values of the > changes along the branches of the phylogeny for the values of shape > variables, centroid sizes and covariates in the original dataset, and the > other with scores for phylogenetically independent contrasts (Felsenstein > 1985) for the same variables.* > > You could retroactively calculate node position in PC space based on the > IndCont and branch lengths. However it may be simpler to run > plotGMPhyloMorphoSpace in *geomorph* in R and extract the ancestral > states (which although are calculated by maximum likelihood using > *phytools* fastanc *) - note that the anc.states matrix returned are > states prior to PCA, so all you'd need to do is: > > all.data <- rbind(two.d.array(mydata), anc.states) # combine tips and > nodes > pcdata <- prcomp(all.data)$x # PCA > > Em > > * ML and weighted squared change parsimony are equivalent assuming BM > model of evolution > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > Emma Sherratt, PhD. > > > Postdoctoral Researcher in the Keogh Lab > <http://biology-assets.anu.edu.au/hosted_sites/Scott/> > Division of Evolution, Ecology & Genetics > Research School of Biology > 116 Daley Road > The Australian National University > Acton, ACT 2601 > AUSTRALIA > > email: emma.sherr...@gmail.com > tel: +61 2612 53029 > mob: +61 4234 19966 > Twitter: @DrEmSherratt <https://twitter.com/DrEmSherratt> > > Caecilians are legless amphibians... > > * __ > (\ .-. .-. /_") > \\_//^\\_//^\\_// > `"` `"` `"`* > > learn more about them here: www.emmasherratt.com/caecilians > > > > > On 17 May 2016 at 01:32, filipe oliveira <filipe.fi...@gmail.com> wrote: > >> Hi, >> >> do you know how to save the PC values of the ancestral nodes estimated >> with Square change Parsimony in MorphoJ? >> >> Thank you. >> Best >> Filipe >> >> -- >> MORPHMET may be accessed via its webpage at http://www.morphometrics.org >> --- >> You received this message because you are subscribed to the Google Groups >> "MORPHMET" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to morphmet+unsubscr...@morphometrics.org. >> > > -- Filipe Oliveira da Silva M.Sc. in Evolutionary Biology (MEME) Uppsala University (Sweden) and University of Munich - LMU (Germany) B.Sc. (Honors). Universidade Federal de Vicosa (Brazil). "In evolution, selection may decide the winner of a given game but development non-randomly define the players" Alberch (1980) -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
