[Phylobase-devl] IDs vs. labels (support for nexml format)

[Ben Bolker]

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~  OK, folks, what do you think?

~  Extend the phylo4 definition?
~  Define an S4 class that extends phylo4 and contains
this additional slot?

~   I will be away next week, but I'm wondering about
people's summer plans and possibilities of revitalizing
the project a bit -- I think we have some reasonably clear
goals set out in the Tracker, and we could do that stuff
and then go for another round of trying to sell the package
to end-users. I was disappointed that the package didn't
(apparently) do what Sang Chul Choi was expecting, and I
have a vague memory that his usage also turned up some
holes.

~  What's the way forward?  Another teleconf?  Everyone going
in and assigning themselves tasks in the tracker?

~  Ben


Aaron Mackey wrote:
|> ~  phylo4 objects have required (integer) Node numbers,
|> required (character) tip labels, and optional (character) node labels
|> (for internal nodes).  Does that satisfy the requirement?
|
|
| nope.  in addition to user-visible labels, I need a slot for unique
| identifiers (which may be non-numeric, and even if numeric may not follow
| the consecutive 1..N ordering of the phylo4 node numbers).  The
identifiers
| are necessary for all nodes, both tips and internal nodes.
|
| But I'd prefer to able to do this generically: to have a (completely
| optional) annotation slot in which to stick things like "nexml node ID"
| and/or any other bits-and-bobs that some other software wants to know
about,
| and phylobase doesn't care about.  Like I said, I can use the phylo4d
| data.frame to store this additional info, but it's not character data,
it's
| meta-data
|
| -Aaron
|
|
|
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