[Phylobase-devl] node retrieval / recapitulation

[Marguerite Butler]

Hi Thibaut and Everyone,

Hope I'm not too late in joining the discussion.

> I am still wondering about distinguishing node/internal. I think a
> former ape user would understand 'nodes' as internal nodes. You may  
> find
> another terminology for the print method. Does 'node' refer to any  
> node
> (tips+internal nodes) elsewhere in the packge (or other required
> packages?). I may be insisting, but as the changes are going to affect
> the whole package...

I'm probably responsible for the creeping in of the node  
terminology.  For me, it is a design issue. The fundamental unit of  
the phylogenetic object is the node (this is how I think about  
abstracting the data). Everything is associated with the node, the  
links to the connecting nodes, the phenotypic data, branch length (or  
time depth), etc.

Tips are in fact nodes (although they are special in the sense that  
they have no descendants and all occur at the same time -- otherwise  
extinct taxa are tips too).

When you think about tree recursion, or tree traversal, it is through  
the nodes.

I understand that there might be some confusion with ape users, but I  
would still rather have the terminology changed to nodes for all  
nodes. Names are important here because it affects the way you think  
about the object, it's special properties, etc. Besides, I think it  
will be a one time thing, people might be temporarily confused, but  
they will quickly figure it out once they see the tree structure or  
the documentation, etc.

> To recap with the nomenclature:
> - "tips", "edges": seems to have a consensus on that
>

I would prefer "branches", only because that's the most commonly  
terminology that we use in the phylogenetics literature, so I think  
that's what users will be most familiar with. I know that  
programmers, mathematicians, and ecologists often use "edges", though.

But this is not a big deal (compared to the nodes issue).

> - "nodes": equals 'internal nodes' (has my vote) /vs/ all nodes  
> (tips +
> internal)
>
Vote for all nodes.

> - "NexusToPhylo4" (and related IO functions): there seems to be a
> consensus for changing the name, and using an argument to specify the
> output; "read.nexus" would conflict with ape, but this may be  
> solved by
> using a namespace (is this overkill?); Hilmar suggested naming the
> function from the content read (phylogeny / comparative data) rather
> than from the format (newick, nexus, ...). I think content is more
> generic, but I find it more visible to have a read.[format].
>

Namespace is a good idea. This package is going to get bigger....

> - naming functions: there seems to be a consensus about the  
> "camelCase"
> (i.e. "lowerCamelCase" rather than "UpperCamelCase").
>
Doesn't matter to me, as long as it's written somewhere (a phylobase  
style guide?)

> Appart from this, one colleague here is presently using/crash-testing
> phylobase - as an enduser -, and I begin to receive good feedback  
> (among
> bunches of "why is this not working?!?"). A good point for us all,  
> I guess.
>

cool!

Marguerite
>

____________________________________________
Marguerite A. Butler
Department of Zoology
University of Hawaii
2538 McCarthy Mall, Edmondson 259
Honolulu, HI  96822

Phone: 808-956-4713
FAX:   808-956-9812
Dept: 808-956-8617
http://www2.hawaii.edu/~mbutler
http://www.hawaii.edu/zoology/

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