[Phylobase-devl] unification of tree data slots

[François Michonneau]

> As part of this process, I did make some user-level changes. Details are 
> below for anyone interested. How should we proceed on determining 
> whether to apply these changes to trunk? We also have Peter's NA->0 
> changes in the queue, and if we adopt both, we'll need to coordinate our 
> merges-to-trunk in a sensible way.

  I haven't really had a chance to test the new functionalities but the
changes you introduce look great, so I agree for merging your branch
into the trunk.

  I also read over the user-visible changes, and I think the choices you
made are all sensible. Thanks for fixing the behavior of merge.data
(this was on my TODO list).

  I enforced the size of the data frames in checkPhylo4Data mainly
because it's what was expected to be returned by the phylo4d
constructor. So, if we would have to use this assumption, then it was a
test to make sure that the user doesn't modify the slots. However, as
the behavior of the constructor has changed, I think it's OK to remove
the code you commented out.

> One somewhat superficial question -- I called the new slot 'data'. Any 
> strong feelings on whether it should be 'tdata' instead?

I slightly prefer 'data'.

  -- François

> Cheers,
> Jim
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