[R-sig-phylo] Calculation of NRI/NTI for large species matrix

2012-05-13 Thread micro buggy
Dear folks, I tried to calculate NRI/NTI for large community matrix (species larger than 20,000, for instance) using Picante. My current PC memory size (12 Gb) can not hold this kind of analyses. Does someone know how to do with this issue? Thanks. Si

[R-sig-phylo] pGLS with populations from diferent localities

2012-05-13 Thread Agus Camacho
Dear all, I am trying to compare environmental vs phylogenetic effects over one trait that has evolved in a single branch. For that, I have 10 closely species that have been collected over 7 localities. The number of localities in which each species has been collected varies from 1 to 3. So some

Re: [R-sig-phylo] Calculation of NRI/NTI for large species matrix

2012-05-13 Thread Steven Kembel
Hi, Scott's suggestion is a good one. Another option would be to split your community matrix into pieces and analyze each separately. This may or may not be feasible depending on the null model you are using. I am in the process of rewriting most phylogenetic alpha/beta diversity methods in

[R-sig-phylo] Distance Matrix for morphological characters, including ?, can it still be euclidean?

2012-05-13 Thread Robert Schenck
I've been trying to create a distance matrix from a dataset of morphological characters, where the matrix contain some characters as ?. Is it possible to get a specifically euclidean matrix from that? When I try to make the distance matrix, I get a what looks to me like a distance matrix,, but it