[Phylobase-devl] misc.
Ben Bolker
bolker at ufl.edu
Thu Dec 18 04:45:25 CET 2008
Brian O'Meara wrote:
> For teleconferencing tomorrow, NESCent recommends Adobe Connect
[snip]
looks fine to me.
I think the noon (EST) meeting should be the official "kick-off",
but there's nothing wrong (recommended?) with people digging
in before that to look at problems of particular interest,
identify/clear bugs, work on stuff they already know they want to
do, etc.. Marguerite is busy, so our full span is from
Steve and Peter (and Jim?) on Pacific standard time (UTC -8 hours)
to Ben, Brian, Hilmar on EST (UTC -5 hours) to Francois
(Central European, UTC+1).
to summarize so far:
Steve Kembel:
* bug and feature requests -- phylo4d and metadata
* tree traversal and ordering
* (check constructors and methods)
Hilmar/Steve: NexML support?
* (synchronize metadata standards)
Ben (ideas -- I don't want to do these all myself!)
* resolve internal node naming convention -- I thought Steve
said we had done this, but I don't see evidence of it
[recap: separate node names from row names, to allow duplicates
turn off automatic node naming
see what breaks when we do this and fix it]
* merge and test PDC's plotting code, especially:
- test against trees with singletons
- try to implement an example of multiple plots on the same page via
simple (?) grid functions
- vertical as well as horizontal phylo4d plots
* implement multiPhylo . Plotting methods ... assume shared
tip data and ID (otherwise we just have a list of trees), allow
shared/nonshared tree topologies (edge matrices) and/or
branch lengths
(Bolker?)
MINOR STUFF/EXTRAS
* resolve recent weird nexus tree example from Mesquite
* more flexible reordering (ability to reorder so plot occurs in
specified tip order)
* debug weird trees created by vcv.phylo/phylo.vcv --
* replicate ancestral state reconstruction plotting in phylo4?
* do we really need the mktime check in ncl code?
* how far has our ncl code diverged? is there anything we
can do to make syncing easier? pass patches upstream??
* add capabilities to readncl?
* RENAME ncl reading functions to be more R'ish?
* fix warnings in ncl code:
e.g. "warning: deprecated conversion from string constant to 'char*'"
* simulation functions? simulate methods for phylo4, phylo4d?
(no -- have to do simulate methods for MODEL FITS, not data objects)
* matrix/graph class conversion for phylo4 objects?
* add data sets -- McPeek 2008, Ives and Godfray 2006, ... ?
(check with comm phylo class)
* develop picante etc. code that uses phylobase?
* check with Andrew Hipp about his needs/wishes?
(survey R-sig-phylo etc.? SurveyMonkey?)
* interface with FigTree?
* is there Mesquite/R work to do?
* improve documentation, vignette, etc.?
>>>> the agenda? We have 11 feature requests <https://r-forge.r-
>>>> project.org/tracker/?atid=491&group_id=111&func=browse> and 1 bug
>>>> <https://r-forge.r-project.org/tracker/?
>>>> atid=488&group_id=111&func=browse> on R-forge, but these haven't
>>>> been
>>>> changed in months. We could add things there and modify their
>>>> priority and assignment, do it more informally over email, throw
>>>> things on a wiki, etc.
>>>>
>>>> Brian
>>>>
>>>> On Dec 8, 2008, at 3:15 PM, Ben Bolker wrote:
>>>>
>>>>> Yes.
>>>>>
>>>>> I was thinking of setting up another time for a preliminary
>>>>> skype/conference/chat meeting, but that feels like overkill.
>>>>> Perhaps we can set an agenda/tentative task assignments by
>>>>> back-and-forth over e-mail.
>>>>>
>>>>> cheers
>>>>> Ben
>>>>>
>>>>>
>>>>> Brian O'Meara wrote:
>>>>>> Hi, all. It appears that Dec. 18-19 are the only days when
>>>>>> everyone who
>>>>>> has filled out the poll can do the minihack (Thursday and Friday
>>>>>> of next
>>>>>> week). See the poll at <http://www.doodle.com/9pndm3xaszh7gpck>.
>>>>>> Shall
>>>>>> we thus schedule the minihack for both of those days?
>>>>>>
>>>>>> Brian
>>>>>>
>>>>>>
>>>>>> On Dec 5, 2008, at 7:44 PM, Marguerite Butler wrote:
>>>>>>
>>>>>>> Hi Folks,
>>>>>>>
>>>>>>> Sorry for the silence. Still teaching my two classes, so I'm
>>>>>>> pretty
>>>>>>> tied up.
>>>>>>>
>>>>>>> Basically next week (week of Dec. 15) and week of Jan 13 are the
>>>>>>> only
>>>>>>> possibilities for me. (I'll be spending some much needed time
>>>>>>> with my
>>>>>>> daughter over Xmas and then I have to get ready for the SICB
>>>>>>> meetings
>>>>>>> in the first week of Jan. (I'm back to work Jan 12, but things
>>>>>>> will be
>>>>>>> pretty nuts that day, so Jan 13 is the first day for me).
>>>>>>>
>>>>>>> Mike Alfaro and I are going to be teaching two sessions at
>>>>>>> SICB, a
>>>>>>> first day for complete beginners in R and a second evening
>>>>>>> session o
>>>>>>> comparative analysis in R, so if there is anything you'd like to
>>>>>>> show
>>>>>>> off, please let me know. Hopefully I can get stuff ready in
>>>>>>> time to
>>>>>>> get feedback from the developers:).
>>>>>>>
>>>>>>> Feel free to go ahead without me on the Hackathon, though, if my
>>>>>>> schedule is a problem.
>>>>>>>
>>>>>>> Marguerite
>>>>>>>
>>>>>>> On Dec 5, 2008, at 12:26 PM, Peter Cowan wrote:
>>>>>>>
>>>>>>>> The list was cc'd, and Steve has already filled out a slot in
>>>>>>>> the
>>>>>>>> 'doodle'.
>>>>>>>>
>>>>>>>> peter
>>>>>>>>
>>>>>>>> On Dec 5, 2008, at 2:23 PM, Ben Bolker wrote:
>>>>>>>>
>>>>>>>>> For what it's worth, Thibaut sent his apologies --
>>>>>>>>> he's going to start a new postdoc very soon.
>>>>>>>>> (I don't remember if he cc'd this list.)
>>>>>>>>> Marguerite, Steve?
>>>>>>>>>
>>>>>>>>> Ben
>>>>>>>>>
>>>>>>>>> Peter Cowan wrote:
>>>>>>>>>> I've added my schedule to http://www.doodle.com/
>>>>>>>>>> 9pndm3xaszh7gpck
>>>>>>>>>>
>>>>>>>>>> On Dec 4, 2008, at 7:31 AM, Brian O'Meara wrote:
>>>>>>>>>>> On Dec 3, 2008, at 2:47 PM, Steven Kembel wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi all,
>>>>>>>>>>>>
>>>>>>>>>>>>> * chat on the list about a deadline and milestones needed
>>>>>>>>>>>>> for a CRAN release? (My votes: merged plotting code, all
>>>>>>>>>>>>> known
>>>>>>>>>>>>> bugs fixed [I don't actually think that would be hard],
>>>>>>>>>>>>> node-
>>>>>>>>>>>>> labeling
>>>>>>>>>>>>> scheme updated).
>>>>>>>>>>>>> * have one or more additional conference calls?
>>>>>>>>>>>> Discussing this on the list or in a conference call would be
>>>>>>>>>>>> great. I
>>>>>>>>>>>> think we are in pretty good shape for most of these things.
>>>>>>>>>>>> -plotting code should be a straightforward merge of the
>>>>>>>>>>>> summer of
>>>>>>>>>>>> code
>>>>>>>>>>>> branch into trunk
>>>>>>>>>> Agreed this shouldn't take long and might even happen before
>>>>>>>>>> the
>>>>>>>>>> virtual hackathon if I can find a few hours to button up loose
>>>>>>>>>> ends.
>>>>>>>>>>
>>>>>>>>>>>> I will go through the list of bugs/feature requests on R-
>>>>>>>>>>>> Forge and try to clean out the requests that have been dealt
>>>>>>>>>>>> with. If
>>>>>>>>>>>> others have fixed bugs/feature requests go ahead and change
>>>>>>>>>>>> their
>>>>>>>>>>>> status to resolved.
>>>>>>>>>>>> -The node-labeling scheme has been updated already unless
>>>>>>>>>>>> there
>>>>>>>>>>>> were
>>>>>>>>>>>> further changes needed.
>>>>>>>>>>>>
>>>>>>>>>>>>> * an ambitious plan: have a "virtual hackathon" sometime
>>>>>>>>>>>>> between now and mid-January, where we all agree to the best
>>>>>>>>>>>>> of our abilities to spend the same day or two investing
>>>>>>>>>>>>> a significant amount of hacking time ... we could have
>>>>>>>>>>>>> one or two 'plenary sessions' a day and do Skype/chat
>>>>>>>>>>>>> in between ... what do you think?
>>>>>>>>>>>> This sounds like a great idea, I'd be interested, will have
>>>>>>>>>>>> some
>>>>>>>>>>>> time
>>>>>>>>>>>> over the 'holidays' to work on this. What are people's
>>>>>>>>>>>> schedules
>>>>>>>>>>>> like
>>>>>>>>>>>> - would a brief call sometime in the next few weeks work?
>>>>>>>>>>> I'm generally unconstrained, as we're not traveling for the
>>>>>>>>>>> holidays.
>>>>>>>>>>> We can set up a poll to schedule a conference call once we
>>>>>>>>>>> have a
>>>>>>>>>>> general idea of when people can talk. I've started a poll
>>>>>>>>>>> about a
>>>>>>>>>>> mini-hackathon itself at http://www.doodle.com/
>>>>>>>>>>> 9pndm3xaszh7gpck .
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Phylobase-devl mailing list
>>>>>>>>>> Phylobase-devl at lists.r-forge.r-project.org
>>>>>>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/
>>>>>>>>>> phylobase-devl
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Ben Bolker
>>>>>>>>> Associate professor, Biology Dep't, Univ. of Florida
>>>>>>>>> bolker at ufl.edu / www.zoology.ufl.edu/bolker
>>>>>>>>> GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc
>>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Phylobase-devl mailing list
>>>>>>>> Phylobase-devl at lists.r-forge.r-project.org
>>>>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/
>>>>>>>> phylobase-devl
>>>>>>>>
>>>>>>> ____________________________________________
>>>>>>> Marguerite A. Butler
>>>>>>> Department of Zoology
>>>>>>> University of Hawaii
>>>>>>> 2538 McCarthy Mall, Snyder 405
>>>>>>> Honolulu, HI 96822
>>>>>>>
>>>>>>> Dept: 808-956-8617
>>>>>>> Lab: 808-956-5867
>>>>>>> FAX: 808-956-9812
>>>>>>> http://www.hawaii.edu/zoology/faculty/butler.html
>>>>>>> http://www2.hawaii.edu/~mbutler
>>>>>>> http://www.hawaii.edu/zoology/
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Phylobase-devl mailing list
>>>>>>> Phylobase-devl at lists.r-forge.r-project.org
>>>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/
>>>>>>> phylobase-devl
>>>>>>>
>>>>>>
>>>>>> ________________________________
>>>>>> Brian O'Meara
>>>>>> NESCent
>>>>>> Durham, NC
>>>>>> http://www.brianomeara.info
>>>>>> ________________________________
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------
>>>>>> -
>>>>>> --
>>>>>> ---
>>>>>>
>>>>>> _______________________________________________
>>>>>> Phylobase-devl mailing list
>>>>>> Phylobase-devl at lists.r-forge.r-project.org
>>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/
>>>>>> phylobase-devl
>>>>>
>>>>> --
>>>>> Ben Bolker
>>>>> Associate professor, Biology Dep't, Univ. of Florida
>>>>> bolker at ufl.edu / www.zoology.ufl.edu/bolker
>>>>> GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc
>>>>>
>>>>> _______________________________________________
>>>>> Phylobase-devl mailing list
>>>>> Phylobase-devl at lists.r-forge.r-project.org
>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/
>>>>> phylobase-devl
>>>>
>>>> ________________________________
>>>> Brian O'Meara
>>>> NESCent
>>>> Durham, NC
>>>> http://www.brianomeara.info
>>>> ________________________________
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Phylobase-devl mailing list
>>>> Phylobase-devl at lists.r-forge.r-project.org
>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/
>>>> phylobase-devl
>>> _______________________________________________
>>> Phylobase-devl mailing list
>>> Phylobase-devl at lists.r-forge.r-project.org
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/
>>> phylobase-devl
>>
>> ________________________________
>> Brian O'Meara
>> NESCent
>> Durham, NC
>> http://www.brianomeara.info
>> ________________________________
>>
>>
>>
>> _______________________________________________
>> Phylobase-devl mailing list
>> Phylobase-devl at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/
>> phylobase-devl
>
>
> ________________________________
> Brian O'Meara
> NESCent
> Durham, NC
> http://www.brianomeara.info
> ________________________________
>
>
>
> _______________________________________________
> Phylobase-devl mailing list
> Phylobase-devl at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/phylobase-devl
--
Ben Bolker
Associate professor, Biology Dep't, Univ. of Florida
bolker at ufl.edu / www.zoology.ufl.edu/bolker
GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc
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