[R-sig-phylo] Imposing backbone constraints in phylogeny reconstruction?

to impose backbone constraints? For example, I want to specify in the model that clade/species A and clade/species B have be ancestral to clade/species C. Is there a way to do this using maximum likelihood in R (I'm using phangorn), and in MrBayes? Thanks! Scott Chamberlain [[alternative

[R-sig-phylo] Why no branch lengths on consensus trees?

- read.tree(ex2.tre) tree3 - read.tree(ex3.tre) trees - c(tree1, tree2, tree3) trees_con - consensus(trees) trees_con Phylogenetic tree with 4 tips and 3 internal nodes. Tip labels:[1] Strix_aluco Asio_otus Athene_noctua Tyto_alba Rooted; no branch lengths. Thanks, Scott Chamberlain

Re: [R-sig-phylo] Why no branch lengths on consensus trees?

-furcation is meant to imply. (Rather: there was evolution, but we aren't very certain about the branching pattern.) But, MrBayes does provide average lengths of some kind. Best wishes, Daniel On 21/11/2012 15:13, Scott Chamberlain myrmecocys...@gmail.com wrote: When making a consensus tree using

Re: [R-sig-phylo] Why no branch lengths on consensus trees?

Dear Joe, Thanks for your feedback on this question. I will go read those pages you mentioned. Scott On Wed, Nov 21, 2012 at 5:19 PM, Joe Felsenstein j...@gs.washington.eduwrote: Daniel Barker wrote: What should branch lengths on a consensus tree represent? Scott Chamberlain had

[R-sig-phylo] Extinction series in bipartite

series that I desire. Thanks, Scott Chamberlain Simon Fraser University [[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] Extinction series in bipartite

Apologies, meant to send to the R-ecolgy list serve! Scott On Thursday, July 12, 2012 at 10:22 AM, Scott Chamberlain wrote: Hello, I am interested in calculating the consequences of removing species from a bipartite network, specifically removing species from the least-connected

[R-sig-phylo] Estimating heritability with sire-offspring regression

, but how do you specify the correct weight Thanks, Scott Chamberlain [[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] Add names to a list in R, and count matching numbers

here'a an example of what i am guessing you want a - list(1,2,3) b - list(4,5,6) for(i in 1:length(a)) { a[[i]] - c(a[i], b[i]) } a On Fri, Dec 9, 2011 at 9:26 AM, charlotte.ndir...@unil.ch wrote: Dear All, I would like to do 2 things. First, I want to add 30 different family names to a

[R-sig-phylo] Simulating a phylogeny with outgroup on long branch

! Scott Chamberlain Rice University [[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] Simulating a phylogeny with outgroup on long branch

of Massachusetts Boston web: http://faculty.umb.edu/liam.**revell/http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://phytools.blogspot.com On 10/13/2011 5:32 PM, Scott Chamberlain wrote: Hello, I want to simulate two types of phylogenies: one normally done with, for example

Re: [R-sig-phylo] Finding distances between tree nodes

require(ape) tree - rtree(10) dist.nodes(tree) dist.nodes gives you pairwise distances between all nodes and tips, then you can just pick out the one you want from the output matrix HTH, Scott On Monday, July 18, 2011 at 5:26 AM, Liutauras Rusaitis wrote: Hello, We're using the Ape

Re: [R-sig-phylo] Assigning node ages to a tree, revisited

about R to debug a script. I thought I'd send this to the list in case someone other than Gene Hunt or Scott Chamberlain has had a go at using this script. Thanks in advance, Roger [[alternative HTML version deleted]] ___ R-sig-phylo

[R-sig-phylo] Felsentsein's contrast LRT

one LRT result in the output even if you have say 3 traits. If you are interested in contrasts and a LRT for all pairwise relationships of the 3 traits, do you just run analyses 3 different times, each with the pair of traits you are interested in? Thanks, Scott Chamberlain

[R-sig-phylo] Felsenstein's 2008 AmNat complete method in R?

This is mostly directed towards Dr. Paradis, but here goes. I realize that ape computes the Felsenstein contrasts that incorporate Felsenstein's within species variance. However, does anyone have code in R for doing the complete method proposed by Felsenstein, including the likelihood ratio

[R-sig-phylo] Phylogenetic correlation

Dear R users, I am trying to compare correlation's among traits without phylogeny and with accounting for phylogenetic history (each data point is a species mean trait value). There is no clear predictor and no clear response variable between two traits. I thought that regression through

[R-sig-phylo] reading nexus file from treebase?

Hello, I can't get read.nexus (ape) or readNexus (phylobase) to read nexus files downloaded from treebase with URLs parsed from xml files. I can't manually edit each file as I want to read a lot of these files. Is there an easy fix? One of the files is copied below. Thanks! Scott

[R-sig-phylo] R interface to treebase.org?

Hello, Are there any packages, or known functions for downloading trees from treebase.org? Thanks, Scott Chamberlain [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch

Re: [R-sig-phylo] mntd and mpd without community data

in the number of taxa in trees. You may want to use several indices in concert. ~Dan Rabosky On Mar 17, 2011, at 8:45 AM, Scott Chamberlain wrote: Hello, I am curious if it is appropriate to calculate mntd (mean nearest taxon distance) and mpd (mean pairwise distance) in the picante

[R-sig-phylo] Assign node ages to a tree

Hello, We have trees for which we have estimated node ages for many nodes (but not all nodes in any one tree). We would like to assign node ages to the trees, and then later transform branch lengths according to node ages. How does one assign node ages in R? Thanks, Scott Chamberlain

Re: [R-sig-phylo] Assign node ages to a tree

://www.graemetlloyd.com/methdpf.html. Again, this was designed for paleontological applications, so it might not get you exactly what you need. The code may be a useful starting point, though. Best, Gene On 3/11/11 10:01 AM, Scott Chamberlain myrmecocys...@gmail.com wrote: Hello, We have trees

[R-sig-phylo] system() and clustalw2

\, cotton.fas, cottonout.aln)) Thanks!!! Scott Chamberlain sessionInfo() R version 2.12.2 (2011-02-25) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] phyloch_1.4.48

Re: [R-sig-phylo] Comparing the topology of two trees

There is also SH.test (Shimodaira-Hasegawa test) in package phangorn And the Icong index by de Vienne which only compares topology (See this website: http://www.ese.u-psud.fr/utilisateurs/devienne/index.html) -Scott On Thursday, March 3, 2011 at 11:37 AM, John Cumbers wrote: Hi Alastair,

[R-sig-phylo] Multiple sequence alignment in R?

Hello, Is clustal multiple sequence alignment implemented in any R packages, or is there an easy way to call ClustalW on your hard drive from R, perhaps with system() Sincerely, Scott Chamberlain Rice University, EEB Dept. [[alternative HTML version deleted

[R-sig-phylo] Ultrametricize?

, but in the 32 bit version the by column names are Var1 and Var2 for some reason pairwisedists - merge(melt(cophenetic(tree)), melt(cophenetic(tree2)), by = c(X1, X2)) Sincerely, Scott Chamberlain Rice University, EEB Dept. [[alternative HTML version deleted

Re: [R-sig-phylo] Simulate discrete characters on tree constrained tophylogenetic signal K

that you're obtaining the amount of signal desired. Ah yes, this applies primarily to quantitative traits, for qualitative characters things change a bit. Enrico Emmanuel Paradis escribió: On Fri, 28 Jan 2011 17:20:57 -0600 Scott Chamberlain myrmecocys...@gmail.com wrote

[R-sig-phylo] Testing topological similarity between trees

/index.html). de Vienne et al. created this website to calculate Icong, but I need to compare a lot of phylogenies and would like to do so from R. Thanks very much! Sincerely, Scott Chamberlain [[alternative HTML version deleted]] ___ R-sig