[Phylobase-devl] stalled ...
Peter Cowan
pdc at berkeley.edu
Thu Jan 15 23:34:18 CET 2009
On Jan 14, 2009, at 12:58 PM, Ben Bolker wrote:
>
> So -- where are we?
At this point, I think we should make all the backwards incompatible
changes we've been discussing. Everything else can be deferred as far
as I'm concerned.
> 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.
I'd still rather have -1 than NA, there are cases when have the NA is
a problem but it's useful to have an nrow(edge) == nNodes(). Is there
a reason for keeping NA aside from inertia?
>>
>> 5. make the naming-convention changes as recommended
>
> NOT DONE. Volunteers? Francois wanted some plurals to
> be kept ...
I think this should be a priority. Nothing is worse than having
commands "disappear" when updating to a new version. So before we
release an 'official' version we should pick final names.
>> 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'd be okay with deferring this. It won't be surprising to users if
we make this better in the future right?
>> I propose that we DELAY:
>>
>> 1. updating ncl to the newer version (unless Brian has this
>> all ready to go)
>
> AGREED.
Also 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.
>
I'd be okay with deferring this as well. This is an enhancement that
won't break older code right?
> 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 ...
I can take a look at this, sometime next week probably. We should
also decide how we are going to handle newlines for the vignette. I
think that I've been soft wrapping and Ben has been hard wrapping,
which causes havoc with svn. Do you have a preference Ben?
Cheers
Peter
>
> _______________________________________________
> Phylobase-devl mailing list
> Phylobase-devl at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/phylobase-devl
More information about the Phylobase-devl
mailing list