[Phylobase-devl] labels() and other questions

Thibaut Jombart jombart at biomserv.univ-lyon1.fr
Thu Feb 28 12:11:31 CET 2008

Hi phylobasists,

1) considering the current implementation of labels() labels(x) returns 
the tip labels of 'x'), I was thinking that I would prefer to have it 
return the labels of all nodes and tips, that is, associating a label to 
each number in @edge.
Anyony voting against this modification, or having an advice?

2) Another small concern I have is about the way functions returning a 
component or a simple information about a phylo4/phylo4d are named:
we have a "hasNodeLabels", a "nTips", or a "rootNode" but we have 
"NodeLabels" and "EdgeLength" (not "nodeLabels" and "edgeLength") to 
give a few examples. This is annoying when looking for a function... 
like typing "node" then [tab][tab] does not list all 'node' functions. 
Another related issue is about already existing functions, i.e. from the 
required packages. Looking for node labels, I was mislead by ape's 
functions "tiplabels", "nodelabels" and "edgelabels" which actually do a 
different job (add labels to a plot).

In an ideal world, I guess, we would be using a generic 
way-of-naming-functions... any idea about what we can do in the real world?



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