[R-sig-phylo] spp taxonomy to phylo object

Hi all, I would like to take taxonomic groupings of species and produce a phylo (phylo4, etc.) object. Does anyone have any suggestions on where to start or has written a script that I could edit to work with my data? Below is an example of the data. Thank you! Matt The data are in order

Re: [R-sig-phylo] Ordering barplot of traits to match tree

Hi All, For another way, below is code that uses the ade4 library (phylog objects) to plot a barchart next to a phylogenetic tree. It is based on the dot.chart.phylog function... I am not sure how well it will work for your data, but it has worked well for most of what I have thrown at it.

Re: [R-sig-phylo] Phylogenetic correlation in relative abundance data

Here is generalized R Code translated from what Tony wrote in Matlab for the paper. Matt Pennell please feel free to respond to me off list for help with your problem. It takes time to set up the model. I have not had time to put it on picante. Emmanuel if you want to use it for ape that is

Re: [R-sig-phylo] algorithm for maximum and minimum phylogenetic diversity

Might also want to look at expected.pd in picante from: J.P. O’Dwyer, S.W. Kembel, and J.L. Green. 2012. Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities. PLoS Comput Biol 8(12): e1002832. Good luck! Matt On Thu, Nov 13, 2014 at 1:12 PM, Eliot Miller

[R-sig-phylo] Phylogenetic Signal in Internal Node Data

Hello, Is there a method that can test for phylogenetic signal in data associated with the internal nodes of a tree rather than data associated with tree tips? Thank you! Matt -- Matthew R. Helmus, Ph.D. Integrative Ecology Lab