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?

ore 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 Slater [he/him/his]

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] 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] fitContinuous-Early Burst Model

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 National Museum of Natural History

Re: [R-sig-phylo] brunch

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 of Ecology and Evolutionary Biology University of California

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

, Brasil. tree.jpeg___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Graham Slater Ph. D. Department of Ecology and Evolutionary Biology

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] 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

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

= _) 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 On Mar 4, 2011, at 7:45 AM, Liam J. Revell wrote

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

. 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 gsla