[Phylobase-devl] Planning the next release of phylobase

David Orme d.orme at imperial.ac.uk
Mon Feb 25 10:53:01 CET 2008

Hi Peter,

I was thinking a branch was the way to go - until it either works or  
seems like a blind alley!

I did start playing with some code and will post it in the new branch.  
I am writing lectures and teaching for a couple of weeks so will be a  
bit quiet


On 25 Feb 2008, at 07:21, Peter Cowan wrote:

> 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.
> Peter
> 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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