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

Ben Bolker bolker at ufl.edu
Wed May 28 19:49:12 CEST 2008


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~  I may be confused, but ...
~  phylo4 objects have required (integer) Node numbers,
required (character) tip labels, and optional (character) node labels
(for internal nodes).  Does that satisfy the requirement?
We had extensive discussion, not followed through on, about reorganizing
node numbers & label schemes -- I believe the final decision was that
node names would NOT be assigned automatically, would NOT be required to
be unique, and (hence) would NOT be used as the rownames of the data
matrix -- but I don't think that has been implemented.  Nevertheless,
I think you shouldn't (?) have any problems if you set the node and
tip labels appropriately ...

~  Ben


Aaron Mackey wrote:
| Last week I spent some time working on "read.nexml" and "write.nexml"
| functions to support IO in nexml format (see: www.nexml.org), a modern
| replacement for NEXUS.
|
| These functions are now working (minimally), but they have a disturbing
| feature: while nexml trees have both an identifier and (optional)
label for
| each node in a tree, phylo4 objects have only one "slot".  Thus, a
tree read
| from nexml cannot be fully represented by a phylo4 object (and so
cannot be
| accurately "round-tripped".
|
| Is there any ability for additional "annotation" on phylo4 nodes?  I
realize
| I can co-opt a phylo4d data.frame for this purpose, but that seems to mix
| the character data with the "metainformation" of a node annotation.  Could
| the phylo4 object model be simply extended to have an identifier and
| (optional) label slot?
|
| Thanks for your thoughts,
|
| -Aaron
|
|
|
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