@Drew_Lab So true. We have let those humanities PhDs dominate the barista job market for so long. Time to bring it back to the sciences!
@researchremix So appropriate because Random house just acquired Penguin.nytimes.com/2012/10/30/bus…
RT @xieyihui: a statistician is a data scientist who does not know he is a data scientist because he never reads twitter
@xieyihui @eddelbuettel @hadleywickham brilliant. I'll go with this definition.
@eperlste it's dreary out so I'll skip driving across the bay and party tomorrow instead.
@eperlste right. But looks like @jasonpriem won't get there till 10 and a couple of others I know canceled. Might also wait till 2mrow.
@eperlste I'll try to make it out there tonight since my earlier plans got canceled. What time you folks getting there?
@researchremix Was going to ask if you & @jasonpriem were going. I can't get there till 830 but might skip if all the cool kids don't go.
@labroides unfortunately most papers are just that. COME ON PEOPLE TELL ME MORE DEETS ABOUT THIS COOL SHIT SO I CAN DO IT.
Either DM or email me your idea at karthik dot ram at gmail.
Ecology & Evolution peeps interested in data sharing/open science, drop me a note if you want to contribute an article. library.queensu.ca/ojs/index.php/…
@rmounce sent.
my attempt at creating an image labels for ggplot2 legend.
stackoverflow.com/a/13148768/313… #rstats #ggplot2
@naupakaz @ethanwhite @tpoi pandoc foo.tex -o foo.txt. This generally works.
@jonesor I use it all the time. Solarized is now part of every syntax highlighting tool.
@yoavram awesome! I've been needing a good slide for explaining the need for DVCS. This is perfect!
I always worry about Markdown's future. But after reading this I'm a little more optimistic. codinghorror.com/blog/2012/10/t…
@boudicca Thanks for organizing last night and for the drinks!
@researchremix @CameronNeylon Nice work you two! See you both next week.
rmounce Anyone interested in #datasharing #datareuse #synthesis or #phylogeny might well be interested in our new paper biomedcentral.com/1756-0500/5/574
@rich_ rnorm(99999999999999999) should heat your processor enough and get the fans going to dry that up.
@Stew neat. On a related note, I'm hoping to wrap up rAltmertic this week and demo it at the PLOS ALM next week.
duffy_ma I'm looking for a technician/lab manager for my aquatic/disease ecology lab! Job ad: umjobs.org/job_detail/756…
jonesor When I say "Earl Grey" you say "yes please"… When I say "Ooh" you say "long"… #timefortea youtube.com/watch?v=eELH0i…
hollybik Moving towards workflow schemes for scientific analyses (e.g. iPython notebook) - will enable transparency and reproducibility #OAweek12
jasonpriem If you're in the Bay Area, don't miss the first #altmetrics hackathon Nov 3-4 at @PLOS! altmetricshackathon2012.eventbrite.com
ReaderMeter Inspiring crowd and talks at the kick off meetup of bay area #opendata, thanks to @boudicca and @codeforamerica for being such great hosts
@gangleton @zachwill open data meetup group. 3 ten minute talks but the plan is to go to a bar nearby after it ends.
None of the folks I know at @codeforamerica are at their open data meetup. Looking at @zachwill and Serena.
@brookeborel much better realizing you've been writing all day but haven't eaten. #donethat
Headed out to see @wilbanks talk at @codeforamerica #opendata
hmason Yay @github! githubarchive.org is amazing data to play with.
@datatelling @shashashasha ah right. I've heard this elsewhere too. But the company is also quite young.
@davidwhogg @github @openscience that would be brilliant and I'd love to see that day. But, baby steps.
davidwhogg we should be able to submit papers to the #arXiv and to #journals by just giving a "git clone" command #openScience (cc @github)
@datatelling @shashashasha I'm sure people have faded away from Github but do you mean no one intentionally deleted their acct?
Drew_Lab Slides from the lecture on the #ImpostorSyndrome up on @figshare. Feel free to share (acknowledgements appreciated) shar.es/c4XBV
@KTInvasion slide = slice.
@KTInvasion So 2 to a bazillion measurements can be referenced by 1 variable. You can slide, dice, transform, facet, whatever by that 1 var.
@KTInvasion You can collapse a dataset with bazillion individuals x bazillion measurements on each into a bazillion x 3 dataset.
@KTInvasion because it is easier to slice and apply functions to long shaped data that wide shaped data. 1 col vs n cols.
@KTInvasion A is easier for data entry. B is easier for transforming data, applying functions and making faceted plots. R makes A->B easy.
@rstudioapp @hadleywickham nice! So are we ---> ropensci.org
@hadleywickham @rstudioapp Looks pretty neat! Bootstrap?
matthewmccull On Git 1.8.0, the default behavior changed:
“git push will warn about upcoming change until you set this var.”
bit.ly/T6O1tb
victoriastodden I'm co-organizing a conf on reproducibility in science in Dec - Peter Norvig and GitHub's @timothyclem keynoting. Woot! icerm.brown.edu/tw12-5-rcem
@mrgunn is there a link to his work?
xkcd charts in d3. dan.iel.fm/xkcd/
my nerdy side is pleased. #d3js
hadleywickham ggmcmc: new package for visualising mcmc results with ggplot2: xavier-fim.net/packages/ggmcm…, by Xavier Fernández-i-Marín #rstats
@distribecology @recology_ @hadleywickham Did this fix it for you? gist.github.com/3908799#commen…
@phdpqc @tpoi @ethanwhite @trashbird1240 Fantastic!
victoriastodden Open source tool to visualize your python scripts, communicate and better understand code: pythontutor.com from pgbovine.net
@CMastication But ok, I’m definitely intrigued.
@CMastication More cores not always = faster computation. For work that I do, it levels of at 96.
@CMastication Seems completely silly. The IO transfer across that many cores will negate any added benefit of that much power.
One of the many joys of working from home. Coding/writing in my back yard. #trythisathome pic.twitter.com/FxyZW9Td
@ethanwhite Love their work too. I need to connect with @fperez_org and talk about some python /R image analysis ideas.
@researchremix @ORCID_Org I'm always embarrassed by all of my code all the time. So, I'm like way way ahead of my peers, right?
Downloading 150 gigs of simulation data from @NICS high performance storage system. Data transfer speed makes it look like black magic.
@recology_ Something you might enjoy. commitlogsfromlastnight.com
A vintage photo of E.B. White composing a tweet. freecabinporn.com/post/337097906…
But srsly, this is one way to finish that manuscript.
@DavidJohnGibson @figshare @ORCID_Org Don't listen to @ethanwhite This mean you are now the protagonist in the new Susan Orlean book.
@recology_ @rstudioapp But how? embed it inside the gui?
@researchremix no worries. Just checking in.
@Impactstory @researchremix Are all your new API changes done? Can I hack away again?
@duffy_ma Darwin had impostor syndrome long before it was cool! Mention that in your lecture, @labroides!
@datatelling What's your panel about? Is there a link to it?
@SeemaSheth Awesome! Thanks for the heads up!
SO BADASS --->> @hadleywickham: @joshua_ulrich nice! I'm working on better profr vis with d3, like had.co.nz/profr/d3/profr… #rstats
@maximolly @datatelling congrats! this is great.
@carlystrasser People were complaining that I look nothing like the Inundata logo. :)
@fonnesbeck @ucfagls @recology_ @ethanwhite Nice to render md correctly on GH for web display. html requires gh-pages which confuses ppl.
@ucfagls @recology_ @ethanwhite @fonnesbeck @EliSwede The only downside is Github md != pandoc md for tables. :(
@ucfagls Thanks! Just figured it out. These render nicely. stackoverflow.com/questions/4546…
smart people -> @iEvoBio: Introducing the iEvoBio 2013 Committee: @kcranstn @Laura_Kubatko @hdeus @trayc7 @carlystrasser @Dr_Bik @ncellinese
hadleywickham new version of httr, web APIs made easy web in #rstats, blog.rstudio.org/2012/10/14/htt…
Scicombinator is super neat! bitwise.r12.railsrumble.com #altmetrics
@moclanmomo The article is OA but the journal made a mistake. Grab a pre-print here: ropensci.org/resources/ (bottom of page)
@noahWG Surely you’ve seen this: individual.utoronto.ca/somody/quiz.ht…
@IHStreet @Pettorelli +1. Seriously contemplating leaving academia in the next year. Hoping to find another way to keep doing science.
@distribecology @recology_ I think I win this round of hipsterest coffee shop. pic.twitter.com/b7SxyUhw
@IHStreet @Pettorelli agreed. But the problem is so pervasive in STEM that we are reaching a breaking point.
@distribecology There is one guy here at the arbor cafe with a Sony Vaio. We're all giving him dirty looks. #maccity
Many more @rOpenSci packages are either on CRAN or will soon get there. Look at all the green on this page! ropensci.org/packages/
@recology_ @ethanwhite @fonnesbeck @EliSwede Anyone know if pandoc supports multi-markdown tables? I also hate lack of tables in mdown.
birbigs I want to live in the Quiet Car of life.
Fun fact: I begin nearly all weekends with a todo list titled "Fires burning" as immortalized in this painting. bukk.it/shitsonfire.jpg
. @recology_ is a R machine. Two packages off to CRAN the same day!
Great perspective on work-life balance and gender inequality in academia by @Pettorelli sciencecareers.sciencemag.org/career_magazin…
couldn't agree more.
rOpenSci ritis, our #rstats wrapper to the Integrated Taxonomic Information Service (or ITIS) was just sent to CRAN, code: bit.ly/HyWEsx
@msanclem @MiriamGoldste Can I blurb the book? "Total…garbage". or maybe I should save that for Miriam's garbage patch book.
@Impactstory Will there be altpetizers at this event? maybe some altisanal beer?
@MiriamGoldste I always use Frontier when I travel to/from CO. I like them a lot.
eperlste If the victors of the Tenure Games have no incentive to change and everyone else gets killed, how does academia evolve?
@duffy_ma I get science done at a much slower pace and I don't even have a baby. #hangsheadinshame
@melissaterras Love it. I bet Governor mittens will give us all professor jobs.
The myth of making tenure (or finding a TT job) is now officially folklore. …miainchildrenspicturebooks.tumblr.com/post/335104222…
@recology_ @fonnesbeck But every once in a while you get a group of collabs all on the same page. #noword
If you ever have to ftp a git managed project, here is a neat little tool for that: github.com/resmo/git-ftp
@kwren88 wow, @GrunerDaniel gets the red carpet. Never seen anyone listed alone on a #FF tweet.
Note: Don't ever mess with @MiriamGoldste. Here's why: youtu.be/l5P4ZiBzoQg?t=…
The first paper on an @rOpenSci package is out! Check out @cboettig and Duncan's Treebase paper onlinelibrary.wiley.com/doi/10.1111/j.…
Hey @mtodd!
A girl just asked me how often I rebase my commits. What the hell I don't even...WTF @github
Someone at the @github meetup offered me a R consulting job at 240/hr. holy shit.
I'm at a @github meetup. Can't handle. So. Much. Nerd.
@ethanwhite (wrong handle). FYI, I used our arXiv paper as an example of collaborative writing for a Cal talk. inundata.org/ecolunch/#GitH…
@ethanwhile FYI, I used our arXiv paper as an example of collaborative writing for a Cal ecolunch talk. inundata.org/ecolunch/#GitH…
@GrunerDaniel But welcome!
@GrunerDaniel wow, Dan. a bit surprised to see you on Twitter.
ReaderMeter Join us on October 24 at Code for America HQ for the inaugural Open Data Bay Area meetup meetup.com/Open-Data-Bay-… #opendata #bigdata #okfn
Rejected manuscripts eventually do find better homes. sciencemag.org/content/early/…
@eperlste Sure you don't want another hit? I'll sell you some 52.28 for cheap. #justkidding #altmetricsalltheway
@arielwaldman Feeling the same way in the east bay. Fighting it with upbeat music and not looking out the window.
PLOSALM #Altmetrics Hackathon, Nov 3 in SF. Hosted by @Impactstory, @PLOSALM. Spread the word & come join us in the fun! altmetricshackathon2012.eventbrite.com
This is exactly where I need to go, far away from the internet, to get a bunch of writing done. ----> freecabinporn.com/post/333655334…
@duffy_ma and look how fancy you turned out! Well done on the interview!
@ethanwhite @recology_ Good call. They announced it a year after I started using it. Scott should apply. They take calls 4 times a year.
@ethanwhite @recology_ Of course they said that! They need to justify keeping their jobs! ;)
@recology_ @ethanwhite I sunk in over 2K of personal funds on EC2 early on. Uni should share cost of large clusters, thro NSF and open it up
@ethanwhite @recology_ agreed. This is silly. HPC centers are not fragile. I know way more about this than my last two PIs combined.
@revodavid A true nerd would have sent this at 13:14:15 ;)
@msanclem always.
@ethanwhite Cool, I didn't notice it posted elsewhere. I was lamenting earlier that I couldn't comment directly on your arXiv version.
@ethanwhite If you guys revise it, I'd be happy to help edit/cut down the revision.
@recology_ Looks really amazing. Cool work.
@zachwill You people are working on an API for rising sun? I love that brewery. +1
@ethanwhite Just read your arXiv paper. Looks great but your section on VCS describes only centralized ones, not distributed ones like Git.
@phdpqc @trashbird1240 Great, thanks! Now I have to write the authors and old fashioned email.
Am i missing something or is it not possible to comment on a arXiv pre-pub?
@mrgunn and not a peep in Berkeley. At least this was a reminder to bring my laundry in.
@phylogenomics somebody got a new iphone ;)
@jasonpriem Glad R is on your brain and you also seem to be rubbing shoulders with Kanye!
@ESA_org You really need to move on from Allen Press. The system is broken and the longer you wait, the harder it’ll get.
@datatelling Indeed, I'm finally excited that NSF recognizes more of my work.
@LizNeeley What dept? zoology?
@emble64 multicore as in the R package?
@distribecology @nceas @recology_ Are decisions due soon?
@recology_ Love the package but what an unfortunate name.
@recology_ It will show updates on all the ones your watching, all orgs you're a member of, and any issues assigned to you.
@recology_ @prismatic I really like QuickHub for mac for that same reason. I can easily see activity, create repos, etc. from my menu bar.
@labroides It’s quite impressive with all those sideways people. Are you at the Hogwarts library?
@JacquelynGill I don’t list them contributed talks in detail since it is just cv padding. I condense those into one sentence with links.
@zachwill @codeforamerica Nice, you people do good work.
markus_eichhorn 3yr research fellowships at Uni of Nottingham, with up to £25k p.a. grant bit.ly/RprCc3. Keen ecologists get in touch!
@hadleywickham nice! looking fwd to it. Is there a major new feature in the update?
Loving oh my zsh to keep track of branches and commit status from my terminal prompt. #git pic.twitter.com/gmIOW1v7
@Impactstory nice! I'm giving a talk on Monday and added impactstory.it Still have enough time to update it!
@ibartomeus @cjlortie @ethanwhite hear hear
Just finished my slides for a Monday talk on a Friday. Not sure I'm ok with being so organized.
@profjsb I see what you did there.
@ninamehta pamfax.biz/en/ worked well for me the last few times i had to deal with a fax machine.
researchremix It's official! Now NSF biosketches "may include... publications, data sets, software, patents, and copyrights" and more nsf.gov/pubs/2013/nsf1…
datadryad After 14-Jan-2013, NSF biosketches to list "products" incl. datasets, software, &etc and not just pubs is.gd/km8oao h/t @ethanwhite:
@phdpqc @tpoi @ethanwhite @trashbird1240 Fantastic!
@cjlortie @ethanwhite For California: sacbee.com/statepay/
noamross A script I wrote to remove annoying cover pages from PDFs: goo.gl/M4pNu @_inundata
@tpoi @phdpqc @ethanwhite Looks good to me. Added a minor comment to improve readability.
@tmccormick @arielwaldman If your twitter is public, then the favs rss feed can be linked to anything (evernote, instapaper) via @IFTTT
@noamross that would be awesome, thanks!
@arielwaldman solution. Archive your Stellar rss feed (i.e. your favorites) to Instapaper while that is still available.
@arielwaldman But I'm also bummed to lose all the @IFTTT Twitter triggers.
@arielwaldman Nope. Any service that does it would violate the new TOS. To archive, bufffer + kipp is an option to archive your own.
Hey Journals, thanks for adding that coversheet to every PDF! Super helpful infomation and I love spending more time at the printer!
@gigi_rose offline PDFs - yes. Their mobile app is not so great though (or at least the last time I tried using it).
@phdpqc @ethanwhite Centralized would be awesome. Would also be a great way to track and reward people who contribute their time.
@distribecology you are right (i have too many versions of python on this machine). Still a great piece of software though.
@distribecology Works for me with 2.7.2 You should post on the Sublime forum. sublimetext.com/forum/ Pretty sure someone will suggest a fix
Pro tip: Need a really clean house and all chores completed? Get yourself a hard deadline.
openscience Choose a PDF to upload knowminer.at:8080/code-demo/inde… Demo of metadata + entity extraction from scientific PDFs ty @_krisjack
Sublime Text is by far the best editor I've ever used. Such a pleasure for coding and general writing (in markdown). tutsplus.com/course/improve…
@p_schulthess If you need a syntax highlighter for non wp-blogs there are many options.
@p_schulthess On inundata.org? Some outdated plugin called wp-syntax. I need to find time to switch away from wp to Jekyll.
Great interview with Ethan Perlstein. nature.com/naturejobs/sci…
mbeisen if prop 37 passes, i'm going to sue organic farmers and ask them to prove prehistoric farmers didn't use "recombinant DNA techniques"
@trashbird1240 @ethanwhite @phdpqc @tpoi How much does Gitorious cost? Does it have a userbase like Github? Git repos can be self-hosted.
@ttso I’ve fixed it. Do an update and you’ll see total counts gone from the plot. Also added support for other doc types.
@ttso Thanks, I realized that. I’ll fix it in the next update.
@ttso yes, that is correct.
@cjlortie It already exists. I need to write a tool to upload data to @DataUpCDL once i figure out their software.
DataONEorg A new tool in the DataONE ITK: DataUp bit.ly/D1DataUpPR. Released today by CDL, Microsoft, DataONE and... fb.me/2egRyiM3X
ethanwhite Grading workflow for my @swcarpentry class: 1. Update student's repository 2. Execute/read code 3. Comments in text file 4. Commit comments
@cjlortie @DataUpCDL I have the exact same issues with using it. Will have to wait for @DataONEorg goodies.
@jebyrnes I suspect that the Q will get you numerous upvotes but no actual answers.
@ttso Thanks for posting that issue. appreciate it!
@jebyrnes not a geom. Should be a theme. So .. + theme_xkcd()
@jebyrnes and now I see you already posted one for R.
@jebyrnes haha. I woke up and marveled at the SE thread too. Nerds do alike.