Rejecting manuscripts on a Friday night earns you a special place in the VIP room of hell.
Told the nice people at @creativecommons that I release most of my code and data as CC0 and they gave me a CC pin!
What the UC “open access” policy should say: michaeleisen.org/blog/?p=1070 via @mbeisen
@recology_ weren’t proposals due yesterday? or the day before?
@phylogenomics What about those poor publishers who now have to dive into a vault with fewer gold coins? #Scrooge #McDuck
BioMickWatson @ctitusbrown surely you can just use v1, v2, v_final, v_final2 etc etc aka version control
@ctitusbrown @ethanwhite will do!
@ctitusbrown hah. I feel that angst with some non-VCed projects too. Great paper! (I shared my feedback on vcs with @ethanwhite).
@David_Dobbs @DavidQuammen Looking fwd to it! Loved the book. So many colleagues in there.
Turns out something good came out of me wreaking havoc on the sever. Apparently there is a huge bug with R 2.15 and mclapply. Thanks @nics!
@MiriamGoldste I never been either and not going now. But I’m just stalking all the cool ppl coming into town.
@carlystrasser my bad. But I need moar results!
“The user karthik is running computationally intensive R code on *** and has
essentially killed the server.”
oh dear.
mbeisen dear #sfbayarea - when worst weather day of year is 55F and a steady rain, you need to stop complaining
@MiriamGoldste Will you be at AGU next week?
figshare When a #blog post is good enough to be citable: Tree (Structures) of Life shar.es/6unhL #science #blogging
@msanclem I’ll swing by for a day but not in attendance at the conf.
@MiriamGoldste Congrats! big drink for you next time I see you.
@matthewmccull Looks great. Thanks! Know if pandoc supports AsciiDoc?
@davidcblackburn So sorry to hear that. I’ve had similar experiences before and it really sucks.
MT @naupakaz Data Viz in R workshop with @_inundata and @ATredennick submitted too!
@distribecology ouch! hope you’re doing ok.
@hylopsar switch to gridExtra and ggsubplot. I don’t use par anymore.
@jebyrnes @MiriamGoldste I actually own that signed print. Go Miriam!
@thePeerJ Do you open doors at midnight? Will I have to camp out in line with the others?
@GrunerDaniel We totally missed our chance to make serious bank.
eperlste Anyone serious about Open Science reforms in biology should read this new post by @caseybergman: caseybergman.wordpress.com/2012/11/29/acc…
Speaking at 2 (possibly 3) #esa2013 workshops on R/ open data/ data visualization stuff! Exciting.
@epistemographer By the time I woke up all you east coaster took every last one!
Has anyone successfully installed Julia on osx (Mountain Lion specifically)?
@zentree hah. Just found out that they cap out fees at 12 authors. So it would still cost less than PLOS.
Looks like ipython has competition!
glimmer.rstudio.com/yihui/knitr/
Looks fantastic! @yihui #rstats
Why You Should Waste Time Documenting Your Scientific Mistakes
- nextscientist.com/documenting-sc… #labnotebooks #openscience
@emilysdarling Back when I handed mine in, they walked me back to the front office, rang a bell, and said we present to you, Dr. K!
@emilysdarling congrats!
RexHuppke I've been asking her all day, but I'm still not sure if my dog actually knows who a good dog is.
kpk Oh no. Someone sent me a dm, and now I need to spend the next week marking it as read on all my devices.
@thePeerJ Thanks, that’s good to know. It gets tricky when figuring out if we’re going to publish again. choose the lowest tier?next one up?
@mbeisen quantum chromodynamics of solace #rejectedbondtitles
@ficaryl right, I agree. The thought of getting one is certainly tempting. But I’d rather go for dog 2.0 when I’m somewhere more permanent.
@arielwaldman Fantastic collection! Wish I had access to it back when I taught invertebrate zoology!
Today was a total open gangnam style day on the R front. Finished a long complicated analysis and the results are biologically interesting.
But PeerJ would be a boon for solo authors or small groups of collaborators.
PeerJ requires every author to have a membership? Going to be hard to convince so many coauthors. Might be a while before I publish there
@ficaryl Is he yours?? I'll follow you a few more times if that's the case.
I've been contemplating getting a hedgy sidekick myself.
@distribecology “remembering shit that I once figured out”
@Protohedgehog @rmounce @PrincessQuatris Love the typo.
@distribecology More that I have 99 problem over and over again.
@srsupp Can’t believe no one has ever used this hashtag before. You’re on to something here.
srsupp Oh no! My head is detached! #githubproblems #entertainingerrors
Happening a lot lately: I google #rstats issues and find the perfect answer on SO and then realize I wrote it. A year ago. #sigh
Great to see @xieyihui on The Setup.
yihui.xie.usesthis.com
@jasonpriem phew. was about to have an altpanic attack.
@hadleywickham fantastic! thank you.
@snacktavish “oh and my grandmother died. again”
sjGoring Asked authors to include their R code in a @PLOSONE review and they did! Hopefully it will become standard to ask and to comply. #RStats
jeanmadams @JNRMSY @soozaphone @BoraZ most phd students say it's isolating. Blogging can be both cathartic for u & create community for others. IMO.
@jasonpriem @cboettig just as easy. Just edit your page and post templates.
Interesting post on image manipulation w/ #rstats. Not convinced it outperforms python/matlab for real world usecases.
is-r.tumblr.com/post/365866146…
Creative new WWF campaign.
ibelieveinadv.com/2012/11/wwf-po…
Interesting approach to automating note taking + metadata extraction from pdfs using applescript and Skim. chronicle.com/blogs/profhack…
Peter Kareiva’s #ESA2012 talk in press at Biosci. “we are advocating conservation for people rather than from people.”
jstor.org/stable/10.1525…
MikeTaylor Dear Every Other Journal: please emulate PeerJ's policy of not requiring references to be formatted in any specific style at submission time
@noamross @cboettig Looks like @thePeerJ is not requiring the use of any journal styles. That’s a good start.
I could really go for a side of sheeps right about now.
i.imgur.com/eUC9q.jpg
#besttypoever
@naupakaz @ATredennick public gist: gist.github.com/4152709 so please edit/or update as necessary. I believe it’s just 250 words.
@naupakaz @ATredennick There isn’t. Here is an abstract draft I threw together: gist.io/4152709
Obama’s front end team on how they heavily relied on “How Github uses Github to build Github”
net.tutsplus.com/articles/inter…
zachholman.com/talk/how-githu…
ftrain If anyone offers me an open-source alternative I will chop them into tiny pieces and push them to origin master.
@labroides Love that movie. I watch it all the time.
So great to finally meet @fperez_org today! So much more to discuss about #reproducibleresearch
@naupakaz Yes. Full link: ecologyunconference.wikispaces.com/Session+propos…
@naupakaz It’s open ended right now. see is.gd/pnvjjx for proposed plan. @recology_ & @sandramchung are organizing all this.
@naupakaz preferably ggplot2.
ramnath_vaidya List of R packages on Github. docs.google.com/spreadsheet/cc… … Code at gist.github.com/4149899#commen… #rstats
xieyihui among #rstats pkg authors, who has the most impressive name? Duncan Temple Lang, because Duncan {Temple Lang} #bibtex github.com/yihui/knitr/co…
Any ecologists and #rstats folks want to help @ATredennick and me run a workshop on data viz in R at #esa2013? If so, please get in touch.
rOpenSci rvertnet is on CRAN (w/binaries) bit.ly/S8ckdk - Interact with @VertNetOrg data from #rstats
@xieyihui @github I prefer github over CRAN. Easier to maintain and update without anyone grumbling.
@ethanwhite @phdpqc Something so easily solved with today’s tech. Reflow ms if someone wants to print. Journal practices need a full reboot
@ctitusbrown heh. Feel the same way when I'm sitting at a cafe launching jobs on a 100k cluster with the ssh app on my phone.
eperlste You all just crowdfunded a research meth lab! @carolynporco put us over the top!!! Time to record my Gangnam style victory dance
amybpedersen I am looking for a graduate student to work on wild immunology and coinfection in wood mice at the Univ. of Edinburgh. tinyurl.com/bqvsq3g
@researchremix If so, you might be interested in a bunch of new color schemes. github.com/daylerees/colo…
@researchremix You’re a sublime fan too? /adds Heather to secret cool people list.
80% of the cores on my cluster are free right now. This is what pure joy feels like.
@labroides Careful there. Looks like someone snuck in some pizza under your broccoli.
From this view it looks like Nate Silver is hanging out less than 2 miles from my house.
twitter.com/fivethirtyeigh…
figshare @ctitusbrown Not sure why we'd treat any digital object (identifier) any different if we want data to be a first class research output.
@researchremix Isn’t there a term for this? Like programmer’s high or something?
Why I chose @figshare for my homeless manuscripts. is.gd/hwFaDl by @emckiernan13 ᔥ @CelHern #openscience #openaccess
figshare To finally answer the question about what research outputs you can share on figshare, we now have this: figshare.com/article_types #openscience
jasonpriem Congrats #PeerageOfScience on published manuscripts! I love how these cats are hacking the #peerreview system. peerageofscience.org/public/blog.ph…
@alignedleft fantastic! looking forward to reading it!
@recology_ I’ve been using Divvy for ages and like it. Got it once when it was on sale. Super useful.
@labroides This one’s for you: youtube.com/watch?v=eELH0i…
@figshare @Stew @jasonpriem @mendeley_com @IanMulvany already picturing each of you sitting in your branded t-shirts. ;)
@hadleywickham great, thank you!
Fingers crossed that no one schedules jobs for tomorrow and I can haz the cluster all to myself.
@labroides 3 papers, 1 revision, grant proposal, crying into pillow, data crunching, bourbon, R coding.
@labroides didn’t get the memo. It’s barely noon here.
eLife Did you know that most #elife papers include decision letter from reviewing editor? To see, scroll to the end of ow.ly/f1ocT
@hadleywickham Here is a fully reproducible example. gist.github.com/4126403
@labroides 957 individual accounts, 6777 tweets total between Jul15-Aug15 but most during 5 days of ESA>
@labroides If any of those are useful, I can get you a higher res version.
@labroides I has the flu so might not get to it tonight. Here are early figures that might be helpful: github.com/karthikram/esa…
@labroides I has the data. writing it up as a paper. I can give you some figures. when do you need them by?
@mrgunn The calendar in my head is messed up. Yup, next Tuesday.
@mrgunn @boudicca I’d be interested in speaking at one of the open data meetups in the future (early next year).
mrgunn Great #opendata event coming up next week at Mozilla in SF at 6 PM: j.mp/Q1CdOC Open Web Data w/srobertson and Kurt Bollacker
@labroides woof
alignedleft Sample code for “Interactive Data Visualization for the Web” posted: github.com/alignedleft/d3… #d3js
@revodavid I used to do that. Now I use pop clip which gives me paste special everywhere. pilotmoon.com/popclip/extens…
@IceAgeEcologist @sjGoring link?
@hadleywickham This is a bug that has been around for a while though (not new, but just ran into it again).
@hadleywickham ldply(large_list, rbind) fails when list has 80k items. Works fine in 20k increments. progress bar shows 100% though.
@emble64 Clearly Banksy needs to branch out into conference posters!
@sandramchung @ATredennick _ at the wrong end! I emailed with @recology_ about this. Not sure bout overlaps.
A neat list of all datasets available via packages in R.
vincentarelbundock.github.com/Rdatasets/data… #rstats
@ATredennick works fine with 2.6. The API for ST2 is python. I highly recommend the editor for all purpose coding.
A 3D printer is most definitely going into startup costs someday. vort.org/2012/11/20/why…
victoriastodden Oxford workshop on "Big Data: Rewards and Risks for the Social Sciences" oii.ox.ac.uk/events/?id=557
@phylorich yep. You can version control with Git but push anywhere. We do that with @rOpenSci. Git + md + Jekyll. We rsync the site to web.
@phylorich make the last one gh-pages.
@phylorich github repo + markdown + Jekyll +gj-pages = win.
@ATredennick if python played well with Sublime Text 2, I'd highly recommend it. I know @distribecology had had problems with it.
Next time you complete a @Square transaction, try something more exciting than your usual signature. twitpic.com/beqis0
@researchremix hells yeah!
mbeisen once again, closed access journals fucking up my research #TimeToKillThemAll
@eperlste No, ours is done. Your tweet triggered the “For the next hr, $ for $ challenge…” commentary in my head. #toomuchpublicradio
@duffy_ma @DynamicEcology I’ve owned that penguin pooh shirt for almost 7 years!
@kaleidoscopeapp
I currently have the academic version. What would I have to pay to upgrade to Kaleidoscope 2?
@kaleidoscopeapp Is $34.99 also the upgrade price for existing users?
eperlste We have just over 5 days to raise $8,940, and we've raised $825 in the last 24 hours. Help us reach $1,000 today! rkthb.co/11106
@eperlste way to make Twitter feel like NPR during pledge drive. Where is my tote bag and eton radio. ;) #kidding
@yoavram I don’t use Rstudio so I don’t know. But with just knitr+md I use:
```{r foo, results=“asis”}
pandoc.table(mtcars[, 1:2])
```
DataONEorg Join DataONE at the @Neon booth during #AGU2012 and in Hall A-C (Moscone South) for the Thursday am poster session (ID: ED41A-0672).
@hadleywickham Would you then say it’s worth investing time in Rcpp? I rarely use it.
soozaphone @edyong209 I am an eternal optimist. Have to be, otherwise I'd spend all day punching myself in the face.
Cohort visualizer (made with d3) looks really slick. bslatkin.github.com/cohorts/ ↬ @mbostock
procrastinating here: natgeo-gifs.tumblr.com ↬ @edyong209
The complete whopping list of 24 papers rejecting human causation of climate change ↬ @bencubby
jamespowell.org/styled/index.h…
@mbeisen fantastic! Thanks for letting me know.
@labroides Cal does 6K which is kinda cool.
@shaenasaurus Yes. See the last paragraph here: plos.org/publish/pricin… Also check to see if your inst cover OA pub fees (mine does).
mhsorens Useful connectivity collection for the science web integrator: rOpenSci Packages #OpenScience #API via @figshare bit.ly/U8NN9X
gawbul PLOS ONE Launches Reproducibility Initiative blogs.plos.org/everyone/2012/…
@PlumAnalytics I get that. But this is what the last paragraph of the article says.
Pandoc for #rstats (pander) is fantastic! No more messing with the ascii package to generate nice markdown tables.
rapporter.github.com/pander/
Video of data reuse session youtube.com/watch?v=UZtNBD… featuring @figshare @mfenner via @rmounce rossmounce.co.uk/2012/11/17/yet… #solo12
@msanclem They do. Give their trial version a go in that case. I don’t think it has any limitations.
@msanclem If so look into the macheist 4 bundle. Scrivener + other good stuff (e.g. 1.5yr Evernote sub) for $29.
@msanclem Def paid for itself. I don’t use Word so this is great. Are you on a mac by any chance?
@msanclem But it’s nice as a binder for text + some research + drafts. Export only good parts to markdown, then pandoc to pdf with citations
@msanclem I do. but only at the beginning stage. Outline as mindmap, export OPML to Scrivener, flesh out ms a little, export at markdown.
@PlumAnalytics article really says “altmetrics sounds great but it’s not replacing anything anytime soon”.
@yoavram hmm, most new stuff is online. Nothing handy but you can peruse my ggplot2 bookmarks. pinboard.in/u:karthik/t:gg…
@David_Dobbs This is how memes begin: flic.kr/p/dtx4H8
Nice photoset from #solo12 @SpotOnLondon. So many familiar faces.
is.gd/vAZocF (working link this time).
R (video) tutorials for newbies: lauraksuttle.com/resources.html #rstats
@gangleton haha. I’m surprised that any fellows are up this early after last night.
Ben_Sheldon_EGI Two lectureships in Zoology Dept @ Oxford: One in Evolution: zoo.ox.ac.uk/node/376
One in Behaviour: zoo.ox.ac.uk/node/377
tomezard 2 yr #PostDoc with the excellent @arpatoz in Zurich linking phenotypes to population dynamics goo.gl/xNhzv #ecrchat
mfenner Did a little more work on our #solo12hack to create RSS/Atom feed for publications in your @ORCID_Org profile, e.g. sciencecard.org/easternblot.at…
@yoavram @hadleywickham I’d skip 8 and the appendices. There are also many helper packages now that do positioning, themes etc.
@JeromyAnglim +1 for Stan.
@yoavram @hadleywickham no. The last 1/3 of the book is outdated IMO. Early chapters are still very much applicable.
@mbeisen I'll keep a lookout. I live right above Cordonices park.
@gangleton congrats to you and the other fellows. /raises glass.
Nerd sad that I cannot run any more simulations on a Fri night because 95% of all cores are in use.
@yoavram @hadleywickham ggplot2 has undergone lots of changes since then. e.g. opts has been deprecated. + many other changes.
@datatelling ah. Well, before you leave sf and move away for your new gig, we should grab a drink sometime.
silentbicycle "At this hour, I'm more interested in a restful IPA than a RESTful API."
@datatelling did you apply?
nmatasci Last chance to apply to the #phylotastic #hachathon this January at @iPlantCollab in Tucson. iplantcollaborative.org/learn/news/201… #bioinformatics
@hadleywickham @github agreed. I think github is missing out on the very large pool of scientists.
@hadleywickham Very much looking forward to r2d3!
@distribecology @recology_ Good point. MD is easy to teach with no background. knitr requires some fluency.
@recology_ @distribecology I'd vote 2. Git/version ctr/collaboration as 1. Then literature programming for pubs/other docs as the other.
@revodavid Perfect! Thanks very much, David!
@hylopsar neat, thanks! I'll check it out.
@revodavid Do you know of any citable sources supporting the fact that R is one of the most widely used analysis tools in academia?
@hylopsar What is your package called?
So much fail whale at my end today.
@labroides stop oncoming traffic, hug sloth tightly, reattach sloth to nearest tree.
revodavid On average, programs in R are 2x shorter than Python and 4x shorter than C++. Mathematica code is shortest. bit.ly/RZfilt #rstats
@cboettig @omearabrian @rOpenSci @eol awesome! Twitter makes it easy to spot these things early on.
altmetric Foggy with a risk of mathematics: altmetric.com/blog/interacti… more equations = less citations?
@ficaryl Here's a better attempt at explaining the nonsense ;)
theatlanticwire.com/topics/horse-e…
@ficaryl Horse_ebooks is difficult to explain. A bit like a markov text generator but funny in a surreal way. e.g. formspring.me/chrisbarmonde/…
@vitoaguiar Ideally, yes. The data are on a secure cluster and I am not allowed to share my pw. So wondering if I can scp data elsewhere,
@larysar thanks, that's the most reasonable solution short of mailing a hd.
@labroides sure thing. Just paying it forward.
What is the easiest way to transfer 150 gigs of data to a collaborator? Too big for Dropbox. DVDs in the mail?
@labroides crowd fund this thing. I'll throw in a few bucks. This insane postdoc salary is burning a hole in my pocket. But srsly do it.
@ficaryl the juxtaposition of words makes it read a bit like @Horse_ebooks