[Phylobase-devl] Nexus tree parsing

[Steve Kembel]

Hi,

I just updated the phylo4d data structure to eliminate the problem  
with duplicate node labels causing crashes when creating phylo4d  
objects with node data. The phylo4d data now rely entirely on the  
tip.label and node.label slots as opposed to storing duplicates of  
those names in the row.names. You can create phylo4d objects matching  
on your data's row.names or a column containing labels with the  
label.type argument to phylo4d, and you can output the data with the  
labels as a column:
library(phylobase)
example(phylo4d)
print(obj)
tdata(obj)
tdata(obj,label.type="column")

Further testing appreciated. I think I fixed all the dependent  
functions that this change broke, except for the NexusToPhylo4D  
function which I couldn't get working, will wait for Brian's update.  
I'd say go ahead and make any changes on the trunk.

Steve

On Jul 17, 2008, at 7:56 AM, Brian O'Meara wrote:

> I was testing nexus parsing again before a course using R here at
> NESCent, and it now doesn't work (just the tree part, I think). I'm
> having trouble checking out the code again from r-forge, but once
> that's working, I'll see what the problem is. I'll fix it on the
> trunk, unless someone things I should branch it for the change(s).