Re: [R-sig-phylo] Phylogenetic size-correction

2015-06-15 Thread Liam J. Revell
Hi Sergio. You didn't specify what BM vf are, but if: BM-corBrownian(1,phy) ## and vf-diag(vcv(phy)) then, yes, this is correct. There is a function in phytools, phy.resid, that also does this calculation. All the best, Liam Liam J. Revell, Assistant Professor of Biology University of

[R-sig-phylo] Phylogenetic size-correction

2015-06-15 Thread Sergio Ferreira Cardoso
Dear all, I just read this paper: Revell, L. J. (2009). Size‐correction and principal components for interspecific comparative studies. Evolution, 63(12), 3258-3268. There is no coding for R, but it says it can be made using APE. From what I could understand this is as simples as:

Re: [R-sig-phylo] Phylogenetic size-correction

2015-06-15 Thread Sergio Ferreira Cardoso
Hello, I'm sorry for not specifying that. But yes, that's exactly it. Thanks for the help. Cheers, Sérgio. 2015-06-15 12:47 GMT+01:00 Liam J. Revell liam.rev...@umb.edu: Hi Sergio. You didn't specify what BM vf are, but if: BM-corBrownian(1,phy) ## and vf-diag(vcv(phy)) then, yes,

Re: [R-sig-phylo] Standalone version of AWTY

2015-06-15 Thread Daniel Fulop
What about using Tracer instead? It's well-maintained with quite recent versions. [[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

Re: [R-sig-phylo] Standalone version of AWTY

2015-06-15 Thread Peter Cowman
Hi Nicholas, There is actually a new version of AWTY rewritten for R (RWTY) by Dan Warren. Here is a link to the github. As far as I’m aware it is functional. https://github.com/danlwarren/RWTY https://github.com/danlwarren/RWTY Cheers Pete On Jun 15, 2015, at 10:43 AM, Daniel Fulop

Re: [R-sig-phylo] Bug in reorder.phylo() (related to cleaning phylo objects)

2015-06-15 Thread Brian O'Meara
A kludgy solution to achieve Dave's original use case of fixing not-quite-right phylo objects is to do: phy - read.tree(text=write.tree(phy)) It converts the tree to Newick and reads it back in. It's not as good a solution as using a validator (great addition, Emanuel!) to find and fix the

Re: [R-sig-phylo] Standalone version of AWTY

2015-06-15 Thread Matt Pennell
Hi, There is a new R implementation of AWTY https://github.com/danlwarren/RWTY Haven't used it myself but I think this will probably alleviate this issue. Cheers, Matt On Mon, Jun 15, 2015 at 7:43 AM, Daniel Fulop dfulop@gmail.com wrote: What about using Tracer instead? It's

Re: [R-sig-phylo] Bug in reorder.phylo() (related to cleaning phylo objects)

2015-06-15 Thread David Bapst
Hi Brian, I was already aware of the read.tree(write.tree()) fix, however I've run into (corner?) cases where a particular sorting of edges or whatever can lead to a loss of tip taxa using the read.tree(write.tree()) approach; plus, read.tree(write.tree()) gets completely flabbergasted by

Re: [R-sig-phylo] Bug in reorder.phylo() (related to cleaning phylo objects)

2015-06-15 Thread David Bapst
Whoops, I meant a 'function in ape?' -Dave On Mon, Jun 15, 2015 at 10:26 AM, David Bapst dwba...@gmail.com wrote: Hi Brian, I was already aware of the read.tree(write.tree()) fix, however I've run into (corner?) cases where a particular sorting of edges or whatever can lead to a loss of tip

Re: [R-sig-phylo] Bug in reorder.phylo() (related to cleaning phylo objects)

2015-06-15 Thread Liam J. Revell
Hi David. I'm not sure about this, but changing to: tree-read.newick(text=write.tree(tree)) tree-collapse.singles(tree) may work. I believe that write.tree will write trees with singletons read.newick in phytools should be able to read them. All the best, Liam Liam J. Revell, Assistant