Monthly Archives: January 2012

Journey to freedom — a code’s tale of open source license migration

My soft­ware wants to be free. It wants to be seen and used and loved by as many peo­ple as pos­si­ble. When first it heard of open source licenses, it set sail to join the com­pany of great soft­ware in the promised land, but find­ing true free­dom has been a tor­tured jour­ney. In the clutches …

January 31, 2012 – 5:58 pm | By Carl | Posted in Open Notebook Thoughts | Comments (3)

Monday

PDG Con­trol, aside exer­cise Lab group com­mented that opti­mum in Reed model looks unre­al­is­tic due to fre­quency with which it shuts down all fish­ing. This is an arti­fact of not hav­ing extrac­tion costs increase suf­fi­ciently for small catch, and can be eas­ily fixed by increas­ing that cost (c in the profit eq, profits-costs = p*x-c/x) …

January 30, 2012 – 7:38 pm | By Carl | Posted in Stochastic Population Dynamics | Tagged , , | Comments (0)

PDG Control Training Problem II update

Basi­cally we’ve done some sim­ple stuff and now would be a good time to think about tools for some heavy-lifting com­pu­ta­tional chal­lenges stand­ing in the way.  Michael & Jim have been a great help on this, and Jake has also helped with the­o­ret­i­cal under­pin­nings. State­ment of prob­lem We con­sider the impact of uncer­tainty in the …

January 24, 2012 – 4:55 pm | By Carl | Posted in Stochastic Population Dynamics | Tagged | Comments (0)

Tuesday

Resilience sem­i­nar the unhelp­ful resilience of invaded sys­tems (ecosys­tem engi­neers any­one?  Cheat­grass change the fire regime, salt-cedar )  Exam­ples in cheat­grass invad­ing sage­brush, and saltcedar invad­ing cot­ton­woods. Vari­ables on axes?  Prob­lem of dimen­sion­al­ity? resilient to what? Carpenter’s rigid­ity trap (need to elim­i­nate some­thing) vs poverty trap (some­thing is miss­ing) pro­mote a small dis­tur­bance to reset the …

January 24, 2012 – 3:04 pm | By Carl | Posted in Logistics | Comments (0)

Friday (lab group meeting notes)

Theme inspired by Jane Lubchenco’s talk last week: how do we con­nect sci­ence to man­age­ment?  We’re break­ing down this topic, with indi­vid­ual lead­ers for each week, as fol­lows: 1/27: Carl: opti­mal vs. action­able man­age­ment rec­om­men­da­tions 2/3: Jaime/Noam(?): mon­i­tor­ing for man­age­ment 2/10: Alli­son: inform­ing man­age­ment vs. advo­cacy 2/17: Lewis: what types of research are must use­ful …

January 20, 2012 – 5:09 pm | By Carl | Posted in Logistics | Comments (0)

Is your phylogeny informative?

Yes­ter­day my paper   appeared in early view in Evo­lu­tion (author’s preprint),1 so I’d like to take this chance to share the back-story and high­light my own view on some of our find­ings, and the asso­ci­ated pack­age on CRAN.2 I didn’t set out to write this paper.  I set out to write a very dif­fer­ent …

January 19, 2012 – 2:10 pm | By Carl | Posted in Phylogenetics | Tagged , , | Comments (3)

Wednesday — meetings

Alan meet­ing write write write Dun­can Meet­ing Trou­bleshoot­ing S3 and S4 Try adding meth­ods? Chang­ing order on NAMESPACE? Leav­ing ouch off the import list: no errors, but within func­tions, don’t get S4 method. import but don’t depend on ouch: error.  accu­rate, since sim­u­late is left as an s3 func­tion at the user level. What a headache.  See stackQ. …

January 18, 2012 – 11:22 pm | By Carl | Posted in Logistics | Comments (0)

Are open lab notebooks considered prior publication?

This ques­tion invari­ably comes up at some point in any dis­cus­sion of open note­book sci­ence.  This con­cern is usu­ally voiced in ref­er­ence to the high-visibility mag­a­zines, which many sci­en­tists seem to assume will have very restric­tive con­di­tions.  A quick read of their poli­cies shows oth­er­wise.  Here are the links to pre-publication poli­cies of major jour­nals, …

January 16, 2012 – 10:47 am | By Carl | Posted in Open Notebook Thoughts | Comments (7)

Forage Fish course plan

For­age fish win­ter quar­ter ses­sion starts, attempt­ing to write the syn­the­sis man­u­script based on Fall quar­ter. Broke into groups to write sub-sections (2-4pgs) by 15 Feb. wk 3 FF Pop Dyn Carl* & Alli­son wk 4 FF Fish­eries: Patrick*, Jay, Carl wk 5 Mam­mals & birds: Angee,* Jamie wk 6 Preda­tor fish­eries: Jamie,*  Kailin,*  Angee wk 7 …

January 12, 2012 – 1:49 pm | By Carl | Posted in Stochastic Population Dynamics | Comments (0)

Resilience Seminar course plan

Resilience Monte Carlo Sem­i­nar, 11am Tues­days. Val Eviner. Jan 17 Resilience of coral reefs/mangrove systems, Alexander Gaos Jan 24 Resilience of degraded vs. intact systems, Erica Case and Alex Web­ster Jan 31 Novel ecosystems, Ania Truszczyn­ski and Mark Noyes Feb 7 Land­scape configuration, Julia Moore Feb 14 Assisted Migration, Anna O’Brien Feb 21 Design­ing and man­ag­ing for resilience, Sarah McCul­lough and Car­o­line Wright Feb 28 Thresholds/ uncertainty, Matt Meis­ner …

January 10, 2012 – 3:17 pm | By Carl | Posted in Logistics, Seminar | Comments (0)