R Hackathon 2

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Revision as of 17:51, 18 December 2008 by Bbolker (talk)
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mini-virtual hackathon

Held December 18-19 via IRC/Adobe connect/Skype/conference call

Participants: Ben Bolker, Peter Cowan, Francois Michonneau, Steve Kembel, Brian O'Meara, Hilmar Lapp, Klaus Scheipl, Marguerite Butler

To-do lists

Add/correct yours here!

Ben Bolker: work on documentation for ordering rules; fix default node-naming convention (now should be blank)

Peter Cowan: merge GSoC plotting code

Steve Kembel: implement new "bound-root" version of edge matrix. reordering and traversal code.

Brian O'Meara: rename ioNCL interface functions (readNexus [subsumes NexusToPhylo4 and NexusToPhylo4d], readNexusdata (or readNexusData). Step 2: merge in newer version of NCL?

Hilmar Lapp: work on NexML functionality

Klaus Scheipl: ? reordering functions?

Marguerite Butler: gadfly :-)

Francois Michonneau: ?

Design changes

  • assume that all code is order-agnostic: add an @order slot for functions that want to check whether re-ordering is necessary. When re-ordering, actually reorder the edge matrix (rather than having an internal index)
  • add root node to edge matrix explicitly, as in OUCH. Root node has NA for ancestor. It is legacy code's responsibility to strip the root node from the edge matrix. Need to modify as(x,"phylo") coercion to do this.
  • change names of ioNCL interface functions/merge them to readNexus
  • old plotting code will go away (tagged as version 0.4 in SVN), replaced by grid-based GSoC code