[R-sig-phylo] comparing taxa in data and tree

Hi all, I am trying to use the geiger’s treedata function to compare and match the taxa in my data and tree as follows: X - treedata(tr, data) where “tr” is the tree and “data” is the matrix. However, the tips are not found in the data and are subsequently dropped from the tree, getting a

Re: [R-sig-phylo] comparing taxa in data and tree

Hi Jorge, I find that this happens most often when I forget to set the row names of data. Try rownames(data) and if they're not the tip labels, then that's your problem. Graham --- -- Graham Slater Peter Buck

Re: [R-sig-phylo] comparing taxa in data and tree

Many thanks for your useful comments. Indeed the problem was that I forgot to set the row names of my data. Now it works fine! thanks, Jorge To add to Graham's comment, if your trait data is in a data frame, then you need to set the row.names(data) to your taxa labels, e.g. with the

[R-sig-phylo] coalescent trees

Hi all,  Is anyone aware of an alternative in R for the tree simulation: “coalescent contained within the current tree” option in Mesquite? Marcelo [[alternative HTML version deleted]] ___ R-sig-phylo mailing list -

Re: [R-sig-phylo] coalescent trees

Hi Marcelo, I'm not familiar with that specific function in Mesquite but from the explanation I saw on the Mesquite website you may want to check out the package phybase by Liang Liu (http://code.google.com/p/phybase/). It has functions to simulate coalescent trees or DNA sequences from a

Re: [R-sig-phylo] coalescent trees

Hi all. By chance I was trying to figure out the same thing today for my phylogeny methods graduate class. Unfortunately, phybase will not install to R=3.0.0 because it doesn't export a namespace. I have added a NAMESPACE file to phybase posted Mac OS Windows builds (for my class) here: