[Phylobase-devl] labels() and other questions

[Hilmar Lapp]

On Feb 29, 2008, at 3:12 PM, Brian O'Meara wrote:

> I can make the change to use one function with an argument once
> we figure out the new name (read.nexus seems logical) and, if it
> exists in ape or elsewhere, how to deal with the conflict. We could
> use "read.nxs" or "read.nex" which don't conflict with ape


I'm admittedly not a big fan of naming functions by file formats.  
Although that makes a lot of sense to those knowing or using the file  
format, it often doesn't to anyone else. Also, it has a tendency to  
become increasingly misleading if the function gets extended over  
time to read other but similar formats as well (e.g., would you want  
functions read.nexus(), read.nexml(), read.phyloxml(), read.phylip(),  
read.nh(), and read.nhx()?).

My suggestion would be to rather name it by either the data type  
being read (like read.table()), or the data type being returned. For  
example, read.tree(), or read.characters(), or read.phylo().

	-hilmar
-- 
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: Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :
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