[Phylobase-devl] edge data?

[Steve Kembel]

Hi Peter,

> This nifty function keeps track of the trait value for each unit of  
> branch
> length.  That is, if a branch has length 5, there will be five values
> along the branch.  This data seems most logically stored as edge data.
> As of now the phylo4d class does not have an edge data slot.
> Furthermore, the commented out version suggests a data frame, which
> would not work with the variable length data described above, trees
> with differing branch lengths.

I think this might be a fairly esoteric use case that would require  
you to create a custom data structure outside the phylo4d object. A  
list associated with each node would work for what you describe  
(that's what the data structure in picante::evolve.traits is), but the  
size of the lists is arbitrary (e.g. what do you do if the branch  
length is 0.15?). We could modify the phylo4d class to allow lists as  
node.data.

> I forget why we decided against edge data, is this too esoteric of a
> use case?  Any suggestions of a better way to handle the above case?

IIRC we decided that edge and node data were really the same thing  
(both can be associated with a node) and so we didn't need two  
separate sets of data and methods to represent the edges and nodes.

Cheers,
Steve