[Phylobase-devl] node retrieval / recapitulation

[Thibaut Jombart]

Steve Kembel wrote:

>Hi,
>  
>
>>That seems good to me. BTW, what do we intend by 'node'? In a phylo4
>>object, we use 'node' for internal nodes. But printing a phylo4  
>>object,
>>'node' refers to any taxonomical unit. This may be annoying since  
>>users
>>can be using both.
>>    
>>
>
>Good point... actually I realized that Ben earlier suggested we use  
>these categories:
>
>c("all","tips","internal","edges") {where "all"= "tips+internal"}.
>
>I can update labels, tdata, and so on to use the new terminology, we  
>will have to change the names and documentation for some of the  
>methods (nNodes, hasNodeLabels, etc.) as well.
>
>Are there any more decisions to be made about what to call things?
>Tips, internals, nodes, edges
>Descendant, ancestor, sister
>?
>
>Steve
>
>  
>
Hi all,

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...

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

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

- "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].

- naming functions: there seems to be a consensus about the "camelCase" 
(i.e. "lowerCamelCase" rather than "UpperCamelCase").

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.

Cheers,

Thibaut.

-- 
######################################
Thibaut JOMBART
CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive
Universite Lyon 1
43 bd du 11 novembre 1918
69622 Villeurbanne Cedex
Tél. : 04.72.43.29.35
Fax : 04.72.43.13.88
jombart at biomserv.univ-lyon1.fr
http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en
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