[Phylobase-devl] where are we??

Ben Bolker bolker at ufl.edu
Tue Dec 30 19:57:08 CET 2008

  With two days to go until supposed release, we seem to be
stalled again (except for Francois, who just committed a patch
for the "internal", "node", "all" consistency.

  I propose that we:

1. merge my branch (with the aforementioned controversial
ordering)  {Peter, can you help with this if/when we
decide to go for it?}

2. see what we can do to detect & fix problems with unrooted trees:
this includes a lot of Steve's "to do" list (sorting out nodeId,
nNode, etc.)

3. fix problems in node labeling on plots that stem from
the change in edge matrix format (Peter may already have a fix
for this but was waiting on other changes)

4.  PDC proposes that we change the NA in the root-node-row
to (-1) instead; I propose that we add a "dropRoot" function
(which just operates on a raw edge matrix, not on a phylo4
object) to abstract the operation of dropping the appropriate
row (essentially substituting for places where we have na.omit
or edge[!is.na(edge[,1]),] in the code now

5. make the naming-convention changes as recommended

6. with some input from Emmanuel, implement SOME form of
checking/consistency rule for ordering when importing/exporting
from/to ape

  I propose that we DELAY:

1. updating ncl to the newer version (unless Brian has this
all ready to go)

2. adding metadata/annotation slots, although if we know
their GENERAL form it would be nice to add them to phylo4[d]
objects now because adding slots later breaks backward compatibility
of saved objects (but we may just have to bite the bullet and
do it later).  In particular if these were slots of type list()
we could be vague about what we were going to put in (at the
cost of less-strong typing of the objects)

3. everything else ...

Ben Bolker
Associate professor, Biology Dep't, Univ. of Florida
bolker at ufl.edu / www.zoology.ufl.edu/bolker
GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc

More information about the Phylobase-devl mailing list