Participants

Jeremy Beaulieu, Brian O'Meara, Natalie Henriques, Jerry Lu, Liya Wang

Action items

ACTION: Get a list of programs related to discrete trait reconstruction and correlation – will be done by Jeremy Beaulieu (Done, forwarded to Brian and Liya. Brian added a couple more papers)

Agenda

Agenda

• review action items from previous meeting
• discuss Jeremy's literature compilation for the discrete trait reconstruction and correlation
• review progress for WG, project goals and timelines
• open discussion

Minutes (DRAFT)

Discussed progress of group. Core software is working on tree IO, other items, not much Contrast yet. But testing is going on.

Goal is to have engagement team (Liya) up to speed on a method a month or two before core developers need to work on it. Liya helps give priorities from biologists to core developers.

Core shouldn't focus on general file parsing, just getting newick/phylip in (biologists agreed, though think loading Nexus also important). Core software is developing their own Nexus parser.

Clarified a set of decisions about contrasts (when to throw warnings, how to test for polytomies, how to deal with discrete characters, how to handle missing data).

Discussion about independent contrasts, ancestral state reconstruction.

Discussion about whether to do global or local estimators, biologists suggested both.

Liya raised point that since ML can give same results as MP, could use ML infrastructure to return MP ancestral state estimates (responds to a request by Pam and Doug Soltis for parsimony ancestral state reconstruction, though ML will remain the priority)

Clarified that Jeremy's list of ML and Bayes methods includes more info than is needed for ML ancestral state estimation (i.e., it includes info on stochastic character mapping).

New action items

Brian will send Liya info on ancestral state reconstruction intros (lectures, books, etc.)