[Phylobase-devl] where are we??

Thibaut Jombart jombart at biomserv.univ-lyon1.fr
Wed Dec 31 13:25:02 CET 2008

> Hi,
>> 1. merge my branch (with the aforementioned controversial
>> ordering)  {Peter, can you help with this if/when we
>> decide to go for it?}
> +1, prefer the named vector for labels in your branch.
+1 for me too.
> Isn't the controversial ordering already in the trunk? Related to  
> ordering, I couldn't tell if there is a consensus on what to do about  
> edge matrix reordering. Marguerite and Thibaut seemed against edge  
> matrix reordering vs. node ids, others pro or neutral.
Please do not hang the release for this. My strong feeling was about 
using node numbers to define the ordering of node labels. Which seems 
agreed on now. In general, I believe the ordering issue becomes less 
concerning as soon as items are named. Concerning edge matrix 
reordering, I things might be made easier if edges were named 
explicitely (e.g. by the descending node, or with smthg like 
"[ancestor]-[descendent]"). Note that such naming could also be used as 
row names of the edge matrix.
> F
I agree with all other suggestions from Ben.

Best regards,


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