Re: [R-sig-phylo] Measuring Phylogenetic Signal

phylo@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > >> Searchable archive at http://www.mail-archive.com/r- > >> sig-ph...@r-project.org/ > >> > >> > > ___ > > R-sig-phylo mailing

Re: [R-sig-phylo] Zero inflated model accounting for phylogeny

> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r- > sig-ph...@r-project.org/ > -- Manabu Sakamoto, PhD manabu.sakam...@gmail.com [[alternative HTML version deleted]] ___

Re: [R-sig-phylo] fatal error plotting trees

ducible example? Is it as simple as plotting > any tree does it or is it only particular trees? > > Cheers, > -Dave > > On Fri, Oct 28, 2016 at 7:53 AM, Manabu Sakamoto > wrote: > > Dear List, > > > > I'm getting fatal errors when plotting phylo objects,

[R-sig-phylo] fatal error plotting trees

enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Has anyone been encountering this issue, or know what the cause is? thanks, Manabu -- Manabu Sakamoto, PhD manabu.sakam...@gmail.com [[alternative HTML version deleted]]

Re: [R-sig-phylo] statistical tests for phylogenetic independent contrasts

Nehru University, New Delhi > > [[alternative HTML version deleted]] > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at

Re: [R-sig-phylo] Pagel 94 Baysian Version 3 states?

ss?! > > Cheers, > Franz > > > Am 14.06.2016 um 11:17 schrieb Manabu Sakamoto >: > > Hi Franz, > > It is implemented in BayesTraits ( > http://www.evolution.rdg.ac.uk/BayesTraits.html). > I know it's not R, and it's a command line based program, s

Re: [R-sig-phylo] Pagel 94 Baysian Version 3 states?

__ > 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/ -- Manabu Sakamoto, PhD manabu.sakam...@gmail.com [[alternative HT

Re: [R-sig-phylo] estimating the evolutionary rate of a continous trait

://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > > > [[alternative HTML version deleted]] > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org R-sig-phylo@r-project.org>

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

> > >>> <mailto: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-proj

Re: [R-sig-phylo] Identify nodes along a pathway from root to a given tip

Dear Klaus, Thank you very much! I got to Descendants but just missed Ancestors Manabu On 4 November 2014 13:15, Klaus Schliep wrote: > Hello Manabu, > try Ancestors from phangorn. > Regards > Klaus > Am 04.11.2014 08:12 schrieb "Manabu Sakamoto" : > >> D

[R-sig-phylo] Identify nodes along a pathway from root to a given tip

Dear list, I was wondering if there was an existing function to identify all the nodes (e.g., phylo$edge[,1]) along a pathway from the root to any given tip. I've found Descendants in phangorn, but I only want the node IDs from the root leading to a given taxon. Many thanks, Manabu -- M

[R-sig-phylo] Blomberg's K and assumptions regarding independent contrasts

a and branch lengths be the original untransformed values? I have the vague sense that it would be circular to make sure the data/branch lengths conform to BM and then test for deviations from BM by computing K. Or am I wrong to think this way? many thanks, Manabu Manabu Sakamoto, PhD Postdoc

Re: [R-sig-phylo] Phylogenetics predictors

atrix. The number of dimensions or k for cmdscale should be (sqrt(length(distance matrix))-1). Manabu Manabu Sakamoto, PhD BBSRC Postdoctoral Research Associate Department of Earth Sciences University of Bristol Bristol, UK, BS8 1RJ Tel: +44 (0) 117 954 5421 Fax: +44 (0)117 925 3385 Email: m.

[R-sig-phylo] Standardising independent contrasts

the two branch lengths that go into the computation of each contrast? I would greatly appreciate any kind support on this matter. Many thanks in advance, Manabu Sakamoto -- -- M. Sakamoto, PhD Department of Earth Sciences, University of Bristol, Wills Memorial Bui