[Phylobase-devl] Votes/discussion requested

[Steven Kembel]

Hi everyone,

It might be hard to get everyone together at the same time for a  
discussion but it sounds like there are some pressing issues that we  
should vote on/discuss. Can we do this via email? Here are the main  
points listed on the wiki at the moment for voting/disussion, feel  
free to reply and add your vote/opinion on these, and whether you  
think they need to be in the 1.5 CRAN release we are preparing. These  
are taken from the wiki at:
https://www.nescent.org/wg_phyloinformatics/Phylobase_Hackathon

1. Ordering issues translating to/from ape
SWK - I feel like these are issues with ape and not phylobase. I'd  
rather not reorder trees by default on export since maintaining order  
can be useful. Suggest that on import from ape @order = 'unknown'.

2. Deprecate/drop: (a) reorder(phylo), printphylo, $
SWK - fine with dropping them for 1.5. There may also be some orphaned  
functions in the treestruc.R file.

3. Namespace
SWK - no strong opinion, only for 1.5 if they are absolutely necessary  
for things to work properly +/or someone can do this easily?

4. Naming conventions
SWK - sounds good, will keep an eye out and try to follow naming  
conventions for 1.5, thanks for the naming table

5. Rordering conventions at @ and accessor levels
SWK - This is crucial and we should decide soon, needs to be sorted  
out for 1.5. I think that many of the problems we're having with  
labels and reordering are due to the fact that until now we treated  
nodes and edges as interchangable. i.e. we had node labels in edge  
matrix order, but these labels should really be associated with nodes,  
not with edges. This assumption caused things to break once edges and  
nodes were not equivalent (now that root edge is in the edge matrix  
and we allow edge matrix reordering, or for unrooted trees). I think  
we need to be very clear about whether methods are actually operating  
on nodes or edges.
I suggest that edge, edge.labels and edge.lengths (branch lengths) are  
in 'edge' order. Everything else (node labels, tip labels) should be  
in node id order. nodeId can translate between these two orders.  
Reorder can act on the edge* only since the underlying node ids will  
not change.
Best guess on what this means in terms of work for 1.5 - currently the  
constructor, tree_check, print, as methods are at least partly making  
a distinction between nodes and edges and their respective ordering  
but need to be checked. phylo4d, tdata, prune methods probably will be  
broken by this change (they assume nodes = edges when linking data and  
labels to tree?) and need to be updated?

6. vcov/distance matrix translation
SWK - No strong opinion, this seems very useful but maybe not for 1.5?

7. Rooted vs. unrooted trees
SWK - I think many methods were assuming a rooted tree. Should at  
least figure how to check for whether a tree is rooted in a robust way  
in tree_check for 1.5 and make sure print/as methods work properly for  
unrooted trees. Most of the hiccups are related to the previous point  
about edges and nodes not being equivalent, maybe solving the label/ 
reorder/edge/nodeId issues will help solve this?