Esa 2012 Conference

  • My Schedule
  • Meetings/discussion with Don Strong, Tony Ives, Marten Scheffer, Justin Yeakel, Karen Abbott, Jarrett Byrnes, Christopher Lortie.
  • Check in with Paul Armsworth on working group
  • rOpenSci tutorial session (below)
  • tweetup
  • My contributed talk (below)

rOpenSci tutorial, Thursday

A year out from our launch at ESA last year, we presented an introduction and tutorial on rOpenSci. Slides and links to more information are all available at

Slides from my talk, Friday

Twitter Notes (generated from R)

hashtag <- "#ESA2012"
user <- "cboettig"

Generate a list of a user’s conference tweets

tweets <- twListToDF(userTimeline(user, n = 500))
tagged <- grep(hashtag, tweets$text, = TRUE)

Write to file, making links appear as links

text <- tweets$text[tagged]
text <- gsub("(@[A-Za-z0-9_]+)", "<a href=\"\\1\">\\1</a>", 

My twitter notes

[1] “.@luketkelly uses GAMM for species response from time since fire, interval, intensity, etc, then solves SDP for optimal policy #esa2012”
[2] “.@luketkelly optimizes distrib of time since fire to maximize geom mean of biodiversity - better than arithmetic or shannon. #esa2012”
[3] “.@luketkelly on optimal fire histories for conserving biodiversity #esa2012 w/ amazing images from down under”
[4] “Armsworth’s analysis in eco let #esa2012”
[5] “Armswortth shows paying farmers for biodiversity gains is best when spatially targeted & worse with multispecies targets #esa2012”
[6] “Fun at #esa2012 where a physics PhD student presents the experimental study testing the mathematical theories presented by the ecology PhD”
[7] “Yet another Science paper described at #esa2012 resilience session: warning signals in yeast dynamics”
[8] “Michael Pace shows early warning in zooplankton levels in lake ecosystem experiment. #esa2012 Why is cv=1 a special value?”
[9] “David Seekell speaking on conditional #heteroskedacity as an early warning signal of sudden shifts #esa2012”
[10] “See Will’s recent paper for correct link to Doak et al #esa2012 (link pdfs from homepages & help a tweep out!)”
[11] “Notes that portfolio effect is inevitable, cites Dan Doak paper: need different null #esa2012”
[12] “96% of returning CA salmon come from hatcheries #esa2012”
[13] “Portfolio effects in salmon stocks: do fish manage risk better than bankers? Will Satterthwaite up now #esa2012”
[14] “Alex Perkins examines impact of poor mixing in disease dynamics, draws analogy to #esa2012 mixers. Transmission is a very local process!”
[15] “Learn how 2 get data & full text open access literature/metadata through R/#rstats w/ @ropensci 11:30a F150 #esa2012”
[16] “de Roos just showed how total biomass can increase with increased mortality. #Wow. #esa2012”
[17] “de Roos: asymmetry/differences in age/size responses (e.g. biomass production) leads to alternate stable states #esa2012”
[18] “Andrre de Roos shows how ontogenetic assymetry (size structure) breaks basic pop dyn predictions #esa2012”
[19] “Check out @luketkelly ’s talk at #esa2012 Friday (10:20a?) #notetoself”
[20] “#esa2012 Come to the @nceas & @sesync mixer, 6:30 PM-8:00 PM, in conference center rm F150”
[21] “In case you missed the talk or the links, see @jebyrnes slides online #esa2012”
[22] “.@jebyrnes mentions Nielsen’s book on online #openscience. Also see his TED talk #esa2012”
[23] “.@jebyrnes reminds us that we live in the 21st century. "Taking the science conversation online" #esa2012”
[24] “Ruckelshaus @NatCapProject echoes Kareiva’s theme of collaborating with groups you don’t agree with: "I’m with stupid" #esa2012”
[25] “Karevia: Best levers for change are private sector, not public. Don’t testify before congress, but before Walmart & DOW #esa2012”
[26] “Karieva cites G. West on cities and creativity, possibly this paper: #esa2012”
[27] “Karevia channels Sarah Palin: how’s that "hope-y change-y thing going?" #esa2012 need more than talking to congress about ecology”
[28] “Olsen: problem isn’t information, it’s informatics (making sense of information) #esa2012”
[29] “Olsen: cites Karevia, biggest problem is scientists cease to be good listeners. #esa2012 Buisnesses hire improv actors to learn this”
[30] “Randy Olsen: scientists evolved from humans. Split was pretty recent. Still have vestiges of story-telling. Don’t lose them! #esa2012”
[31] “Can find the room by the line going deep into the hallway RT @carlystrasser: .@se_hampton is TEARING IT UP. join the fun A106 #ESA2012” [32] “to be accessible to reviewers RT @rOpenSci: Ecological Monographs now requires data to be deposited prior to publication #esa2012”
[33] “Ben Bolker on the need for off-the-shelf methods: not enough staticians for every ecologist to have a stats buddy 4 custom methods #esa2012”
[34] “#esa2012 stats discussion: "all modeling is exploratory. If you think AIC confirms your hypothesis, you’re wrong"”
[35] “Yeakel uses perturbations/return rate to estimate elasticity, more senstive to fun. form, see #esa2012 #mustread”
[36] “Yeakel cites on nonpar bayes, compares to generalized models #esa2012”
[37] “Excellent #esa2012 session understand vs predict in modelling. Explores ecologist’s v of Breiman’s "Two Cultures"”
[38] “Kellner: Multispecies modelling has biggest impact when including non-consumptive value #esa2012”
[39] “Kellner presents rich model for multispecies management of fisheries, see #esa2012”
[40] “Bobby describing disease modeling: humans are essentially widgets that eventually fail #esa2012”
[41] “Not nearly enough room for the crowd outside Karen Abbott’s talk: what’s so special about alternative stable states? #esa2012”
[42] “#esa2012 @sesync panel live peer-review of audience-submitted ideas. Levin: "It should count: I view social science as subset of ecology"”
[43] “Ray Hilborn "fisheries management is people management" need socio-econ context of ecology. @sesync #esa2012”
[44] “Molly discusses "most important number you’ve never heard of" - Social cost of carbon #esa2012 @sesync ($25/ton is current est)”
[45] “Lopez-Hoffman explores equitable water-rights that conserve ecosystem services, e.g. Colarado river use @sesync #esa2012”
[46] “Levin: cites common-pool resources example from African cattle #esa2012”
[47] “Simon Levin speaking @sesync panel: polycentric appches to international agreements on enviro resources #esa2012”
[48] “#esa2012 @sesync will focus on "wicked problems" (technical term) using theme-driven, interdisciplinary approaches”
[49] “Excellent #esa2012 session intro 2 @sesync: "if you’re familiar with @nceas, you’re familiar w/ synthesis". Now focus on socio-econ + uncert”
[50] “#esa2012 @biocreativity Speaking of art-science collab, don’t forget Dr. Scheffer’s "Critical Transitions, the Movie"”
[51] “Lubchenco discusses NOAA’s effort to create climate services like their drought forecasting software: #esa2012”
[52] “Lubchenco’s Q&A brings with disclaimer about Hatch Act: she is speaking for the agency, not the campaign, and can’t answer some Q’s #esa2012”
[53] “At #esa2011 plenary, Pacala encouraged us to spend some time on policy-rel issues. #esa2012 Lubchenco raises the bar: run for office!”
[54] “For instance, to promote outreach, NOAA workers are encouraged to use social media, see their policy: #esa2012”
[55] “Lubchenco trumpets success of Magnuson-Stevens Act of 2007 ( as the policy which will end overfishing #esa2012”
[56] “Lubchenco discusses examples of ecosystem thinking in policy such as the Ocean Policy Task Force: #ESA2012”
[57] “#esa2012 Lubchenco on the challenge of scale across ecological, social + econ contexts: highlights DeFries 2012”
[58] “Jane Lubchenco, opening plenary of #esa2012, dedicates her talk to economics Nobel Laureate Elinor Ostrom”
[59] “.@mickresearch speaker ready rooms are D134 & F152 7a-7p, by reservation(?) (program pg 7). Looking forward to your talk btw #esa2012”
[60] “#esa2012 is trying to facilitate networking for young scientists by labeling cocktail tables by sub-field during tonight’s reception”
[61] “Off to Portland for #esa2012”

Mentions at conference, (other than retweets)

mentions <- twListToDF(searchTwitter(paste("@", user, sep = ""), 
    n = 300))
with_hashtag <- grep(hashtag, mentions$text, = TRUE)
rt <- grep("RT\\s", mentions$text)
me_not_rt <- with_hashtag[!(with_hashtag %in% rt)]

Again, write the output

text2 <- mentions$text[me_not_rt]
text2 <- gsub("(@[A-Za-z0-9_]+)", "<a href=\"\\1\">\\1</a>", 

[1] “. @cboettig building cost of switching policies into models necessary & provide better outcomes that reduce costs of management #ESA2012”
[2] “. @cboettig most optimal management strategies produce fluctuations that policy makers don’t like - we can model their dislike! #esa2012”
[3] “.@cboettig enthusiastically uniting decision theory and resilience theory for management. Making math exciting! #esa2012”
[4] “Go see @cboettig (Carl Boettiger’s) talk today in E143 at 920 - he gives a great engaging talk #esa2012”
[5] “#FF #ESA2012 @DynamicEcology @labroides @qaecology @cboettig @paulrehrlich @tessafrancis @lizabio @gigi_rose @IngaPLaPuma @sarcozona” [6] “Awesome! MT @cboettig: Fun at #esa2012 where physics student presents experiment testing the mathematical theories presented by ecology PhD”
[7] “.@cboettig says readme.txt is the best way to keep track of dataset versions. Can version control that on github #ESA2012”
[8] “@jasonpriem @_inundata @cboettig Don’t worry- you made an appearance earlier when @totalimpactdev was discussed! #ESA2012”
[9] “@carlystrasser @_inundata @cboettig Sorry to be missing that! #ESA2012”
[10] “We’ve reached the part of the workshop where .@_inundata and @cboettig slamming MATLAB now… #ESA2012”
[11] “@cboettig - let db managers know that you would use a repository + API to share your data with them - move ecology data forward #esa2012”
[12] “.@cboettig: R is a pain to learn. @rOpenSci packages and tools take advantage of your current knowledge base. #ESA2012”
[13] “@ropensci @cboettig: scripting analyses makes science reproducible, repeatable, & creates an analytical workflow #esa2012”
[14] “.@cboettig showing Michener’s Info Entropy Graph: more time passing means less remembered about data #ESA2012”
[15] “@jacquelyngill @cboettig @treebiology @jenedavison would you like to write about #ESA2012 for @Scitable”
[16] “Fun #ESA2012 tweetup. Nice meeting you! @cboettig @MiriamGoldste @SarahBisbing @bonebraking @JacquelynGill @msanclem @luketkelly @edyong209
[17] “Check out @cboettig’s talk at #ESA2012 Friday 9:20 in E143. Unknown unknowns: management strategies under uncertainty & alt stable states”
[18] “@cboettig @luketkelly is at 10:30 on Friday in E144 at #ESA2012. Optimal fire history for conserving biodiversity.”
[19] “#ESA2012 tweetup was a great idea. Nice meeting you guys @cboettig @MiriamGoldste @SarahBisbing @bonebraking @JacquelynGill @msanclem and co”
[20] “Rt @cboettig in case you missed the talk or the links, see @jebyrnes slides online #esa2012”
[21] “@cboettig @ropensci for all other journals too I mean. Why not share the data? #esa2012”
[22] “@cboettig @ropensci agreed. Or at least a subset of data for referees and the readership to access #esa2012”
[23] “@cboettig which leads to the suggestion that we need stats mentors and editors in eeb. #esa2012”
[24] “MT @forestdim: Inspired by @cboettig ’s stardom to tweet. Ppl mistaking me 4 @edyong209. Need 2 now ride the wave of false ID #ESA2012”
[25] “Yay for Baysian stats! MT @cboettig: #esa2012 stats discussion: "If you think AIC confirms your hypothesis, you’re wrong"”
[26] “Why code should be made avail: MT @cboettig Ben Bolker: not enuf staticians 4 each ecologst to have a stats buddy 4 custom methods #esa2012”
[27] “Conversation at #esa2012 Hastings lab dinner: pole dancing at the 2016 Olympics? @Dr_Bik @cboettig
[28] “@cboettig Thanks for the art-science tip! #ESA2012 #biocreativity "Critical Transitions, The Movie" TONIGHT Portland Blrm 251 8-10p”
[29] “Let’s hear it for statistics! MT @ropensci: Check out @rOpenSci developer talks: @_inundata Tues 840a, F150 & @cboettig 920a, E143. #esa2012”
[30] “Not on rOpenSci… MT @rOpenSci: Check out talks by @rOpenSci developers: @_inundata Tues 8:40 am F150 - @cboettig 9:20 am E143 #esa2012”
[31] “Check out talks by @rOpenSci developers: @_inundata Tues 8:40 am F150 - @cboettig 9:20 am E143 #esa2012”