[Phylobase-devl] unification of tree data slots

[Jim Regetz]

Quick reply just about the labels question:

Peter Cowan wrote:
>>> On Wed, 2009-09-16 at 15:17 -0700, Jim Regetz wrote:
>>>> 
>>>> Addendum: In case anyone else's mind happens to wander in this 
>>>> direction, yes, I think a similar argument could be made for 
>>>> combining the slots for tip and internal _labels_ into a single
>>>> label slot, because each label is now unambiguously identified
>>>> by its name (node ID). Seems like the separation is a
>>>> historical artifact? Combining them would simplify the
>>>> corresponding accessor/replace methods, which currently have to
>>>> look conditionally in either tip.label or node.label depending
>>>> on the arguments. And it wouldn't be hard at all to make this 
>>>> change in the code base. Of course, I'm not going to ask for
>>>> the moon *and* the stars, but if someone else proposed it... :)
>>>> 
> 
> Again, I think performance was the reason here.  The assumption that
>  more often than not trees will not have any internal node labels.

That doesn't have to be a problem. What I said about tree data applies 
even more clearly here: only labels that actually exist need to be in 
the vector. So if you only supply tip labels when you create the tree, 
the (unified) label slot would be exactly the same as what we now call 
tip.label. Example with a 3-tip tree:

## actual slot contents -- no internal labels stored
 > phy at label
    1    2    3
"t2" "t1" "t3"

## but the accessors would still "fill in" implied the NAs:
 > labels(phy) ## default type is 'all'
    1    2    3    4    5
"t2" "t1" "t3"   NA   NA

 > tipLabels(phy)
    1    2    3
"t2" "t1" "t3"

 > nodeLabels(phy)
  4  5
NA NA

## now add internal labels
 > nodeLabels(phy) <- c("n4", "n5")
 > phy at label
    1    2    3    4    5
"t2" "t1" "t3" "n4" "n5"

## and remove them again!
 > nodeLabels(phy) <- as.character(NA)
 > phy at label
    1    2    3
"t2" "t1" "t3"

I just quickly wrote up new accessor and replace methods that would 
behave this way. As illustrated above, the replacement method will also 
drop any NA labels it encounters, for efficiency (but obviously attempts 
to do this for tip labels will produce an error).

Jim