Esa 2013 Notes For Week


Co-Leading the Workshop on R, DataONE and open science.

All material on github


  • Ives Plenary

Talking to Dave, Vasilis, Tye,

  • Lunch Vasilis, Ryan Batt

  • 2:30 Chesson L100H / Ryan Batt L100J
  • 3:20 O’Regan L100H
  • 3:40 Adler L100H
  • 4 Yaekel M100HC

  • ropensci meetup, funded by Github. Great turnout, great success. (And rare shot of dev team together in person).
  • Theoretical ecology mixer
  • Hastings Lab dinner

Great discussions with Trevor Hefley on some very nice work dealing with biases in messy data. See Hefley 2013 and 2013b, and more in the works.


  • 8am Carpenter L100B
  • M100IB 8am - 10am
  • 10am meeting Carpenter, see seperate nodes
  • 12am Lunch with Lei Dai
  • 2:50pm Drake L100G

Afternoon inteview with Virginia Gewin on Yeakel’s talk. Remarkable challenge to explain generalized modeling for ecological networks in plain english. Virginia gets all the credit for condensing my lengthy verbage into a tweet size summary. Now out in Nature News

  • Open Science session in evening

Amazing talk and later discussion with Russell Neches.

  • open hardware and 3D printers for scientific research. 3 examples:
  • cheaper than alternatives (water quality monitor on rduino chip, tweets data)
  • More flexible than alternatives: variable depth 96 well plates to automate concentration of sample. (also cheap gel combs)
  • When no alternative exists: measuring gape without harming fish.
  • Avoid Nature’s $9000 APC open access option by including a $1000 new genome. (Genome papers are OA by agreement…)
  • Choose PhD advisor by Bayesian Classifier…


  • 3:20 David Hoover (missed)
  • 3:40 Ingrid

spatial waves maxwell

  • 4pm L Dai 101D

  • 4:20 Anna Gardmark

Explaining lack of recovery / hysteresis

  • Prey competing with (younger life stages of) predators (Bundy Finning 2005 CJFAS, Walters .. , …)
  • Prey predating upon younger life stages of codes (Swan and Sinclair 2000 CJFAS)
  • Prey growth changes due to predation (poor condition, or prey size structure) (vulnerability - deRoos Peerson 2002 PNAS)

  • 4:40 Mark Novak

Kelp-urchin transition. Otters arrival leads to transitions in Vancouver Island set, resulting in shifts (used as training). San Nicolas Island sets transitions on its own, despite otter introduction in process. Spatial transects and 31 years of data, 5 replicate transects for all sites. Bayesian change-point analysis to identify shifts (e.g. see Erdman & Emerson 2012).

Chatting with Mark after talk.

  • SySnc / NCEAS Mixer
  • TweetUp

Discussion of semantics and NeXML with Ben Morris (wrote python parser). Sounds like I need to read semantic web for working ontologist

Excellent discussion with Ethan White on what a Institute for Software Sustainability would do.

  • Training training training. Materials, workshops.
  • Much would be improved with a few best practices: unit tests, version control
  • Google Summer of Code style funding


  • 8am Thurs Dakos
  • Discussion with Ryan Batt
  • Discussions with Lei Dai and Vasilis. Lei’s Science paper data on Dryad (temporal indicators). Get back to Lei on format for this data.
  • Exchange with Bestlemyer - lack of time resolution for warining indicators of spatial study. Data from Ecosphere paper on Harvard’s LTER site.

Excellent discussion with Ben Bolker and Dave Harris on what Software Sustainability Institute would accomplish:

  • Tackling archiving / backports of code. CRAN offers only “current” and “devel”, you’re on you’re own getting older stuff running.
  • Training! Not just for grad students - Ben would attend. More experienced, but self-taught, developers like Ben would come with their own questions and could guide what training they needed.
  • Bringing academics together with experts in hackathon style of improving existing codes would be great.
  • One challenge is maintaining accessibility of code styles so that academics can continue to contribute. e.g. most academic R programmers don’t understand S4 classes, would be a potential barrier.

Van Noorden’s data sharing article out, with quotes by Elizabeth, Wolkovich, Heather, Bill Mitchner, yours truly.

  • Flight out