[Phylobase-devl] labels() and other questions

[Ben Bolker]

Brian O'Meara wrote:

> I'm more than happy to change (or have changed) the IO function names  
> to have them consistent with general R/phylobase style. Ape conflicts  
> may be a problem, there, too (such as read.nexus). There's also the  
> issue of having one input format (nexus) and multiple output  
> structures (tree, data, or tree+data object). Currently, this is  
> handled by NexusToPhylo4, NexusToDataFrame, and NexusToPhylo4D. I  
> don't know the best style: does one add a suffix to indicate the  
> target ("read.nexus.phylo4d"), add the target type as an argument to  
> a single read.nexus function, or some other approach?
> 

   yes.  :-)

   I would vote for a single argument; that way if the function
wanted to do some guessing (on the basis of what was in the Nexus
file) it could ...
   Don't know what to do about the name conflict, though.

    Ben



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