[R-sig-phylo] phylogenetic covariance matrix

()? Is it the covariance matrix divided by the total time? I'll appreciate any help with this. Santiago Santiago Claramunt Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, LA70803 scla...@lsu.edu http://www.museum.lsu.edu/Claramunt/Home.html

[R-sig-phylo] yule.cov

this is happening. The oder issue is that the Log-likelihoods I obtained are smaller than for simple yule model fitted using yule(). Is ape reporting -LogLiks? Thanks in advance, Santiago Santiago Claramunt Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge

[R-sig-phylo] inverting C matrices from Yule trees

() and rcoal() are fine. Any insights on this? Cheers, Santiago Santiago Claramunt Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, LA70803 scla...@tigers.lsu.edu http://www.museum.lsu.edu/Claramunt/Home.html ___ R-sig

[R-sig-phylo] RelTime algorithm

Does anyone know of an imlplementation of the RelTime algorithm ( 1. Tamura K, 2. Battistuzzi FU, 3. Billing-Ross P, 4. Murillo O, 5. Filipski A, 6. Kumar S . Estimating divergence times in large molecular phylogenies. Proc Natl Acad Sci U S A.2012;109:19333-19338.) in R?

Re: [R-sig-phylo] axisChrono and axisPhylo

___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ Santiago Claramunt, Ph.D. Research Associate Department of Ornithology American Museum of Natural History

Re: [R-sig-phylo] Non Parametric PGLS

Hi Julien, Mosimann’s method was proposed for the study of allometry, so it would be strange if it only applies to isometric cases. Can you provide further details or suggest readings? Cheers, Santiago On Jun 18, 2015, at 7:06 PM, Julien Clavel julien.cla...@hotmail.fr wrote: Hi Sergio,

Re: [R-sig-phylo] Non Parametric PGLS

Hi Sergio, If what you want to do is to partition your morphometric data into size and shape components, then you can use Mosimann’s methods which do not require regressions or phylogenetic corrections. Mosimann, J. E. 1970. Size allometry: size and shape variables with charac- terization of

Re: [R-sig-phylo] Measurement error for tips with only 1 measured specimen (OUwie)

Hi Rafael, Your method would underestimate the error associated with values derived from single specimens because those values would have the highest errors, not average errors. What I have done in such cases is to estimate an average standard deviation across species and use that average

[R-sig-phylo] Maximum likelihood time-scaling

Does anyone know a maximum-likelihood implementation that uses molecular sequences to optimizes node ages instead of branch lengths (ala Felsenstein 2008, p. 266)? It sounds like nice idea for using in time calibrations. Cheers, Santiago Santiago Claramunt Associate Curator Department