[Phylobase-devl] labeling order

[Peter Cowan]

On Dec 24, 2008, at 2:17 PM, Marguerite Butler wrote:

> Hi Guys,
>
> Not sure what has happened, and I realize I may not understand. But  
> I don't think it's a good idea to have different positional orders  
> for edge matrix, labels, ID's, etc. I think that would make it  
> really difficult for programmers to understand what is going on.  
> Please see my response in the longer thread "vote for arguments"

Marguerite,

I didn't get your longer message, would you mind resending it to the  
list.  To comment on the label ordering issue.

I think the edge matrix and nodes have been getting confused.  The  
edge matrix is made up of the node numbers.  I think it makes sense to  
put the labels following the order of the node numbers rather than the  
order of the edge matrix.

e.g. it's less surprising to do labels(x)[node#] to get the right  
label, than to have to check it's position in the edge matrix.

my 2 cents,

Peter


> Merry Christmas.
> Marguerite
>
> On Dec 24, 2008, at 7:37 AM, Steven Kembel wrote:
>
>> +1
>> On Dec 24, 2008, at 11:22 AM, Peter Cowan wrote:
>>
>>>
>>> On Dec 24, 2008, at 11:21 AM, Ben Bolker wrote:
>>>
>>>>
>>>> Shall I go ahead and bite the bullet/move to putting & leaving
>>>> underlying representation (@node.label, @tip.label, etc.) in
>>>> node ID order?
>>>
>>> + 1 from me, this is how the reorder methods works.
>>>
>>> peter
>>>
>>>
>>>> Ben
>>>>
>>>> -- 
>>>> Ben Bolker
>>>> Associate professor, Biology Dep't, Univ. of Florida
>>>> bolker at ufl.edu / www.zoology.ufl.edu/bolker
>>>> GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc
>>>>
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