[Phylobase-devl] Planning the next release of phylobase

Peter Cowan pdc at berkeley.edu
Mon Feb 25 08:21:32 CET 2008

If you want to make changes that will temporarily break things, we can  
make a new branch to do that.  If there are different thoughts on how  
to number nodes it's easy enough to make two new branches for both of  
you to work on, until we finalize an approach.

Making branches can be done by navigating to the phylobase folder of a  
clean check out (we don't want to copy of a bunch of build files), and  
running something along the lines of.

svn cp pkg/ branches/nodeNumbering
svn st

Then commit the change.


On Feb 24, 2008, at 10:36 PM, Steve Kembel wrote:

> Hi David,
>> I think with this, the row names in the tdata structures would be
>> the integer ids (which could/would/should be the same as the
>> relevant edge numbers from the edge matrix). This would be a fairly
>> major change though!
> If integer IDs (same as edge numbers from edge matrix) are the way we
> will identify nodes "internally", I could go through and modify the
> check_data code to work either with row.names or a column of labels
> when attaching data to a phylo4d. Rather than breaking the existing
> check_data and tdata functions, I will try to build on the code in
> pdata.R.
> From your email it seems like you've already been working on this and
> have a new node.label structure set up? Could you send around or
> commit the changes you've made to the node.label code?
> Steve
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