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

Hi AnneMarie, The way Paolo suggests would be the best/right way to do this. We're working on some methods for incorporating fossil info in comparative methods and I have some code that will do this that i can send you off-list if you would like. I should add that, at least based on what we'v

Re: [R-sig-phylo] problem calculating independent contrasts

the pics returned would be random. Graham Graham Slater Department of Ecology and Evolutionary Biology University of California, Los Angeles 621 Charles E Young Drive South Los Angeles CA 90095-1606 (310) 825-4669 gsla...@ucla.edu

Re: [R-sig-phylo] more problems with branch names

ero. > Doutorando em Zoologia. > Laboratório de Herpetologia, Departamento de Zoologia, Instituto de > Biociências, USP. > Rua do Matão, trav. 14, nº 321, Cidade Universitária, > São Paulo - SP, CEP: 05508-090, Brasil. > > ___ > R-sig-phylo mailing list > R-sig-ph

Re: [R-sig-phylo] brunch

ctation. Because the contrasts are computed explicitly between pairs of taxa that differ in categorical group membership, you can't model Y as a function of both a discrete and continuous trait. Graham -------- Graham Slater Department

Re: [R-sig-phylo] phylogenetic independent contrasts for MANOVA?

t these models. best, Graham -------- Graham Slater Department of Ecology and Evolutionary Biology University of California, Los Angeles 621 Charles E Young Drive South Los Angeles CA 90095-1606 (310) 825-4669 gsla...@ucla.edu www.eeb.u

Re: [R-sig-phylo] how select optimal phylogenetic trees using R

ld also do this in R. I may well be wrong here though, and BayesTraits may do something more sophisticated. cheers, Graham -------- Graham Slater Peter Buck Post-Doctoral Fellow Department of Paleobiology National Museum of Natural History The S

Re: [R-sig-phylo] fitContinuous-Early Burst Model

log(min.rate) / T where T is the depth of your tree and min.rate is the ending rate. I've found a value of 10^-5 is reasonable in most cases. Graham -------- Graham Slater Peter Buck Post-Doctoral Fellow Department of Paleobiology Natio

Re: [R-sig-phylo] ancestral trait reconstruction and OU model

small. Butler and King (2004) discuss this a little bit more. Graham Graham Slater Department of Ecology and Evolutionary Biology University of California, Los Angeles 621 Charles E Young Drive South Los Angeles CA 90095-1606 (310) 825-4669

Re: [R-sig-phylo] Pruning a tree

ow I do that? > > greets > > Eugen > [[alternative HTML version deleted]] > > ___ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo --

Re: [R-sig-phylo] Pruning a tree

uot;Species", tree$tip.label, sep = "_") -------- Graham Slater Department of Ecology and Evolutionary Biology University of California, Los Angeles 621 Charles E Young Drive South Los Angeles CA 90095-1606 (310) 825-4669 gsla...@ucla.edu www.eeb.ucla.edu/gslater

Re: [R-sig-phylo] Phylogenetic PCA and measurement error

Hi Rafael, You need to mean-center your traits before multiplying by the matrix of eigenvectors. Compute the vector of phylogenetic means (under BM or Pagel’s lambda), subtract each value from the relevant column of Xm and then compute Si. The result should be identical to the scores from your

Re: [R-sig-phylo] is.binary() says "FALSE" after using multi2di()

Hi Pedro, multi2di on this newick string returns a tree of 102 tips with 103 nodes, so you seem to have a badly formatted tree. Plotting the resulting tree with all edge lengths = 1 does not immediately reveal, at least to me, where the issue(s) lie but perhaps it will to you? Graham -

Re: [R-sig-phylo] If my trait X cannot be regressed by body size, how can I rescue residuals corrected by the phylogeny and SE?

rors there. A more direct approach might be to use a phylogenetic Bayesian multi-level model, as implemented in brms or mcmcglmm, where all observations are included and species identity is treated as an effect. I've probably missed something, but I hope this helps... Graham -- Graham Sla