Re: [R-sig-phylo] PGLS, categorical data and regression through origin

Dear Julien, maybe I dont understand your rmodel...but IF your model has one continuous dep. and one categorical (binary) indep. it looks like an ANOVA model: in this case phy.anova() [or phy.manova() if you have 1 dependents] in the R package geiger does it. IF the model is different

Re: [R-sig-phylo] Comparing slopes from regressions and PIC regressions

VERY synthetically The two r-squared are NOT comparable. Taking in to account phylogeny is useful just to partial out data non independence due to shared ancestry, and to perform better tests of significance but the r-sq could be higher or smaller just because of chance. Maybe someone can

[R-sig-phylo] add a group of taxa in a specfied vector of nodes positions

Hi all, I think my question has somthing to do with past posts about add.everywhere() and bind.tree(). If I have a tree and a group of taxa to be added to that tree each of which in a tip-specific position (i.e. each attached to a particular node)and with a particular edge length there is a fast

[R-sig-phylo] covriance matrix internal nodes

Hi all, Having a tree (NOT ultrametric in my case) I would like to extract the phylogenetic covariance matrix including both tips and nodes (like dist.nodes for patristic distances). vcv returns the cov matric just for tips. Someone has a fast way? Thankyou very much Paolo

[R-sig-phylo] diversification analysis for non ultrametric trees

Hi all, I would like to try some diversification analyses using medusa or related methods(gamma stat, Quasse, etc). However, my tree is highly NOT ultrametric as it includes many extinct (and sometimes very old) taxa. From literature it seems that these methods are not applicable to non

Re: [R-sig-phylo] diversification analysis for non ultrametric trees

Hi Emmanuel, Thankyou very much for your reply. In fact the rwb() function (library paleoPhylo; thanks to Thomas Ezard for some extra code) does much of the things I need. Some other methods are not yet implemented for non ultrametric trees. For now... Best Paolo Hi Paolo, The methods you cite

[R-sig-phylo] Pics and multivariate tests in R

Dear all, I write you in order to ask some help in interpreting global multivariate tests using pics of a model including multivariate response and an univariate predictor. I APOLOGIZE IN ADVANCE IF MY QUESTION WILL RESULT TRIVIAL. I found substantial differences using summary.lm(), anova.lm()

Re: [R-sig-phylo] pic() vs gls()

Hi all, Citing http://www.r-phylo.org/wiki/HowTo/Ancestral_State_Reconstruction: Using Felsenstein's (1985) phylogenetic independent contrasts (pic); This is also a Brownian-motion based estimator, but it only takes descendants of each node into account in reconstructing the state at that node.

[R-sig-phylo] cut a tree in a given time interval

Hi all, someone knows a smart coding to cut a tree in order to retain only taxa present in a given time interval bin? Thanks in advance for any suggestion best paolo ___ R-sig-phylo mailing list R-sig-phylo@r-project.org

Re: [R-sig-phylo] ancestral state reconstruction with fixed internal node(s)

Hi AnneMarie, I dont really know if this makes sense; in fact ancestral state reconstruction is an ** a posteriori estimation ** of nodal values starting from tips observations. A trick could be to add a false taxon lnked to that node and giving to it a 0 branch length (i.e. plitomized - you can

Re: [R-sig-phylo] nodes and taxa depth II

Thanyou Nick! it seems there are a lot of useful functions; thankyou very much best paolo Looks like this is solved, but: Awhile ago I decided it would be handy to extract/display all kinds of information from a tree in a table format, with a row for each node. Two of the columns

Re: [R-sig-phylo] nodes and taxa depth II

Hi Emmanuel, This is syncronism! I JUST solved in ONE line using dist.nodes() it seems correct to me; if anyone find a bug ..thanks in advance