[Phylobase-devl] stalled ...

[Ben Bolker]

  So -- where are we?

  From before:

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

  DONE.

> 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)

   DONE.
>
> 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

  NA to -1 switch not made.
  edges now has a drop.root argument (default = FALSE) that
should do this.

>
> 5. make the naming-convention changes as recommended

  NOT DONE.  Volunteers?  Francois wanted some plurals to
be kept ...

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

   NOT DONE. Volunteers?
>
>   I propose that we DELAY:
>
> 1. updating ncl to the newer version (unless Brian has this
> all ready to go)

  AGREED.

>
> 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)

  Could add as list() if we can agree on names for the slots,
how many.

  PS: if someone wants to take a look at the "hard way" simulator
code in section 9 of the vignette and suggest ways that this could
be done more easily (possibly by adding convenience functions and/or
accessors that do the hard work), please feel free ...