Karthik Ram @_inundata

Yay Area / ✈ in transit

November 2012

Rejecting manuscripts on a Friday night earns you a special place in the VIP room of hell.

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Told the nice people at @creativecommons that I release most of my code and data as CC0 and they gave me a CC pin!

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What the UC “open access” policy should say: michaeleisen.org/blog/?p=1070 via @mbeisen

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@recology_ weren’t proposals due yesterday? or the day before?

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@phylogenomics What about those poor publishers who now have to dive into a vault with fewer gold coins?

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BioMickWatson @ctitusbrown surely you can just use v1, v2, v_final, v_final2 etc etc aka version control

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@ctitusbrown hah. I feel that angst with some non-VCed projects too. Great paper! (I shared my feedback on vcs with @ethanwhite).

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@David_Dobbs @DavidQuammen Looking fwd to it! Loved the book. So many colleagues in there.

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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!

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@MiriamGoldste I never been either and not going now. But I’m just stalking all the cool ppl coming into town.

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“The user karthik is running computationally intensive R code on *** and has
essentially killed the server.”
oh dear.

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mbeisen dear - when worst weather day of year is 55F and a steady rain, you need to stop complaining

via Twitter for iPhone (retweeted on 10:40 AM, Nov 30th, 2012 via Tweetbot for Mac)

figshare When a post is good enough to be citable: Tree (Structures) of Life shar.es/6unhL

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@msanclem I’ll swing by for a day but not in attendance at the conf.

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@MiriamGoldste Congrats! big drink for you next time I see you.

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@matthewmccull Looks great. Thanks! Know if pandoc supports AsciiDoc?

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@davidcblackburn So sorry to hear that. I’ve had similar experiences before and it really sucks.

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MT @naupakaz Data Viz in R workshop with @_inundata and @ATredennick submitted too!

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@hylopsar switch to gridExtra and ggsubplot. I don’t use par anymore.

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@jebyrnes @MiriamGoldste I actually own that signed print. Go Miriam!

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@thePeerJ Do you open doors at midnight? Will I have to camp out in line with the others?

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@GrunerDaniel We totally missed our chance to make serious bank.

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eperlste Anyone serious about Open Science reforms in biology should read this new post by @caseybergman: caseybergman.wordpress.com/2012/11/29/acc…

via Twitter Web Client (retweeted on 1:46 PM, Nov 29th, 2012 via Tweetbot for Mac)

Speaking at 2 (possibly 3) workshops on R/ open data/ data visualization stuff! Exciting.

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@epistemographer By the time I woke up all you east coaster took every last one!

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Has anyone successfully installed Julia on osx (Mountain Lion specifically)?

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@zentree hah. Just found out that they cap out fees at 12 authors. So it would still cost less than PLOS.

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Looks like ipython has competition!

glimmer.rstudio.com/yihui/knitr/

Looks fantastic! @yihui

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Why You Should Waste Time Documenting Your Scientific Mistakes
- nextscientist.com/documenting-sc…

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@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!

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RexHuppke I’ve been asking her all day, but I’m still not sure if my dog actually knows who a good dog is.

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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.

via Twitter for iPad (retweeted on 10:55 PM, Nov 28th, 2012 via Twitter Web Client)

@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?

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@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.

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@arielwaldman Fantastic collection! Wish I had access to it back when I taught invertebrate zoology!

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Today was a total open gangnam style day on the R front. Finished a long complicated analysis and the results are biologically interesting.

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But PeerJ would be a boon for solo authors or small groups of collaborators.

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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

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@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.

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@distribecology “remembering shit that I once figured out”

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@distribecology More that I have 99 problem over and over again.

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@srsupp Can’t believe no one has ever used this hashtag before. You’re on to something here.

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srsupp Oh no! My head is detached!

via Twitter Web Client (retweeted on 1:07 PM, Nov 28th, 2012 via Tweetbot for Mac)

Happening a lot lately: I google issues and find the perfect answer on SO and then realize I wrote it. A year ago.

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@jasonpriem phew. was about to have an altpanic attack.

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@snacktavish “oh and my grandmother died. again”

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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.

via Twitter Web Client (retweeted on 9:09 AM, Nov 28th, 2012 via Tweetbot for iOS)

jeanmadams @JNRMSY @soozaphone @BoraZ most phd students say it’s isolating. Blogging can be both cathartic for u & create community for others. IMO.

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cboettig @F1000 indeed! I’d follow @F1000Ecology & @F1000Evolution if they existed

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@jasonpriem @cboettig just as easy. Just edit your page and post templates.

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Interesting post on image manipulation w/ . Not convinced it outperforms python/matlab for real world usecases.
is-r.tumblr.com/post/365866146…

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Interesting approach to automating note taking + metadata extraction from pdfs using applescript and Skim. chronicle.com/blogs/profhack…

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Peter Kareiva’s talk in press at Biosci. “we are advocating conservation for people rather than from people.”
jstor.org/stable/10.1525…

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MikeTaylor Dear Every Other Journal: please emulate PeerJ’s policy of not requiring references to be formatted in any specific style at submission time

via Twitter Web Client (retweeted on 8:41 AM, Nov 27th, 2012 via Tweetbot for Mac)

@noamross @cboettig Looks like @thePeerJ is not requiring the use of any journal styles. That’s a good start.

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I could really go for a side of sheeps right about now.

i.imgur.com/eUC9q.jpg

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@naupakaz @ATredennick public gist: gist.github.com/4152709 so please edit/or update as necessary. I believe it’s just 250 words.

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@naupakaz @ATredennick There isn’t. Here is an abstract draft I threw together: gist.io/4152709

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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…

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ftrain If anyone offers me an open-source alternative I will chop them into tiny pieces and push them to origin master.

via Twitter Web Client (retweeted on 9:10 PM, Nov 26th, 2012 via Twitter Web Client)

@labroides Love that movie. I watch it all the time.

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So great to finally meet @fperez_org today! So much more to discuss about

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@naupakaz It’s open ended right now. see is.gd/pnvjjx for proposed plan. @recology_ & @sandramchung are organizing all this.

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ramnath_vaidya List of R packages on Github. docs.google.com/spreadsheet/cc… … Code agist.github.com/4149899#commen…xts

via Twitter Web Client (retweeted on 2:44 PM, Nov 26th, 2012 via Tweetbot for iOS)

xieyihui among pkg authors, who has the most impressive name? Duncan Temple Lang, because Duncan {Temple Lang} github.com/yihui/knitr/co…

via Twitter Web Client (retweeted on 2:43 PM, Nov 26th, 2012 via Tweetbot for iOS)

Any ecologists and folks want to help @ATredennick and me run a workshop on data viz in R at ? If so, please get in touch.

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rOpenSci rvertnet is on CRAN (w/binaries) bit.ly/S8ckdk - Interact with @VertNetOrg data from

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@xieyihui @github I prefer github over CRAN. Easier to maintain and update without anyone grumbling.

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@ethanwhite @phdpqc Something so easily solved with today’s tech. Reflow ms if someone wants to print. Journal practices need a full reboot

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@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.

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eperlste You all just crowdfunded a research meth lab! @carolynporco put us over the top!!! Time to record my Gangnam style victory dance

via Twitter for iPhone (retweeted on 10:57 PM, Nov 24th, 2012 via Tweetbot for iOS)

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

via Twitter for iPhone (retweeted on 11:57 PM, Nov 23rd, 2012 via Tweetbot for Mac)

@researchremix If so, you might be interested in a bunch of new color schemes. github.com/daylerees/colo…

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@researchremix You’re a sublime fan too? /adds Heather to secret cool people list.

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80% of the cores on my cluster are free right now. This is what pure joy feels like.

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@labroides Careful there. Looks like someone snuck in some pizza under your broccoli.

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From this view it looks like Nate Silver is hanging out less than 2 miles from my house.

twitter.com/fivethirtyeigh…

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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.

via Twitter for iPhone (retweeted on 3:37 PM, Nov 22nd, 2012 via Tweetbot for iOS)

@researchremix Isn’t there a term for this? Like programmer’s high or something?

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figshare To finally answer the question about what research outputs you can share on figshare, we now have this: figshare.com/article_types

via Twitter Web Client (retweeted on 10:02 AM, Nov 22nd, 2012 via Tweetbot for Mac)

jasonpriem Congrats on published manuscripts! I love how these cats are hacking the system. peerageofscience.org/public/blog.ph…

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@alignedleft fantastic! looking forward to reading it!

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@recology_ I’ve been using Divvy for ages and like it. Got it once when it was on sale. Super useful.

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@figshare @Stew @jasonpriem @mendeley_com @IanMulvany already picturing each of you sitting in your branded t-shirts. ;)

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Fingers crossed that no one schedules jobs for tomorrow and I can haz the cluster all to myself.

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@labroides 3 papers, 1 revision, grant proposal, crying into pillow, data crunching, bourbon, R coding.

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@labroides didn’t get the memo. It’s barely noon here.

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eLife Did you know that most papers include decision letter from reviewing editor? To see, scroll to the end of ow.ly/f1ocT

via Twitter Web Client (retweeted on 9:51 AM, Nov 21st, 2012 via Tweetbot for Mac)

@labroides 957 individual accounts, 6777 tweets total between Jul15-Aug15 but most during 5 days of ESA>

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@labroides If any of those are useful, I can get you a higher res version.

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@labroides I has the flu so might not get to it tonight. Here are early figures that might be helpful: github.com/karthikram/esa…

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@labroides I has the data. writing it up as a paper. I can give you some figures. when do you need them by?

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@mrgunn The calendar in my head is messed up. Yup, next Tuesday.

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@mrgunn @boudicca Great. I hope to be at the event tomorrow.

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@mrgunn @boudicca I’d be interested in speaking at one of the open data meetups in the future (early next year).

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mrgunn Great event coming up next week at Mozilla in SF at 6 PM: j.mp/Q1CdOC Open Web Data w/srobertson and Kurt Bollacker

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alignedleft Sample code for “Interactive Data Visualization for the Web” posted: github.com/alignedleft/d3…

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@revodavid I used to do that. Now I use pop clip which gives me paste special everywhere. pilotmoon.com/popclip/extens…

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@hadleywickham This is a bug that has been around for a while though (not new, but just ran into it again).

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@hadleywickham ldply(large_list, rbind) fails when list has 80k items. Works fine in 20k increments. progress bar shows 100% though.

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@emble64 Clearly Banksy needs to branch out into conference posters!

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@sandramchung @ATredennick _ at the wrong end! I emailed with @recology_ about this. Not sure bout overlaps.

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A neat list of all datasets available via packages in R.

vincentarelbundock.github.com/Rdatasets/data…

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@ATredennick works fine with 2.6. The API for ST2 is python. I highly recommend the editor for all purpose coding.

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A 3D printer is most definitely going into startup costs someday. vort.org/2012/11/20/why…

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victoriastodden Oxford workshop on “Big Data: Rewards and Risks for the Social Sciences” oii.ox.ac.uk/events/?id=557

via Twitter Web Client (retweeted on 8:20 AM, Nov 20th, 2012 via Tweetbot for iOS)

@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.

via Tweetbot for iOS in reply to rgfitzjohn

@phylorich github repo + markdown + Jekyll +gj-pages = win.

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@ATredennick if python played well with Sublime Text 2, I’d highly recommend it. I know @distribecology had had problems with it.

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Next time you complete a @Square transaction, try something more exciting than your usual signature. twitpic.com/beqis0

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mbeisen once again, closed access journals fucking up my research

via Twitter Web Client (retweeted on 5:50 PM, Nov 19th, 2012 via Tweetbot for Mac)

@eperlste No, ours is done. Your tweet triggered the “For the next hr, $ for $ challenge…” commentary in my headio

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@duffy_ma @DynamicEcology I’ve owned that penguin pooh shirt for almost 7 years!

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@kaleidoscopeapp
I currently have the academic version. What would I have to pay to upgrade to Kaleidoscope 2?

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@kaleidoscopeapp Is $34.99 also the upgrade price for existing users?

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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

via Twitter Web Client (retweeted on 4:35 PM, Nov 19th, 2012 via Tweetbot for Mac)

@eperlste way to make Twitter feel like NPR during pledge drive. Where is my tote bag and eton radio. ;)

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@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])
“`

via Tweetbot for Mac in reply to yoavram

DataONEorg Join DataONE at the @Neon booth during and in Hall A-C (Moscone South) for the Thursday am poster session (ID: ED41A-0672).

via Hootsuite (retweeted on 10:40 AM, Nov 19th, 2012 via Tweetbot for Mac)

@hadleywickham Would you then say it’s worth investing time in Rcpp? I rarely use it.

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soozaphone @edyong209 I am an eternal optimist. Have to be, otherwise I’d spend all day punching myself in the face.

via Twitter Web Client (retweeted on 8:20 AM, Nov 19th, 2012 via Tweetbot for Mac)

Cohort visualizer (made with d3) looks really slick. bslatkin.github.com/cohorts/@mbostock

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The complete whopping list of 24 papers rejecting human causation of climate change ↬ @bencubby
jamespowell.org/styled/index.h…

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@mbeisen fantastic! Thanks for letting me know.

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@shaenasaurus Yes. See the last paragraph here: plos.org/publish/pricin… Also check to see if your inst cover OA pub fees (mine does).

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mhsorens Useful connectivity collection for the science web integrator: rOpenSci Packages via @figshare bit.ly/U8NN9X

via bitly bitlink (retweeted on 1:11 PM, Nov 18th, 2012 via Tweetbot for Mac)

gawbul PLOS ONE Launches Reproducibility Initiative blogs.plos.org/everyone/2012/…

via Twitter for Websites (retweeted on 9:21 AM, Nov 18th, 2012 via Tweetbot for Mac)

@PlumAnalytics I get that. But this is what the last paragraph of the article says.

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Pandoc for (pander) is fantastic! No more messing with the ascii package to generate nice markdown tables.

rapporter.github.com/pander/

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@msanclem They do. Give their trial version a go in that case. I don’t think it has any limitations.

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@msanclem If so look into the macheist 4 bundle. Scrivener + other good stuff (e.g. 1.5yr Evernote sub) for $29.

via Tweetbot for Mac in reply to msanclem

@msanclem Def paid for itself. I don’t use Word so this is great. Are you on a mac by any chance?

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@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

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@msanclem I do. but only at the beginning stage. Outline as mindmap, export OPML to Scrivener, flesh out ms a little, export at markdown.

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@PlumAnalytics article really says “altmetrics sounds great but it’s not replacing anything anytime soon”.

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@yoavram hmm, most new stuff is online. Nothing handy but you can peruse my ggplot2 bookmarks. pinboard.in/u:karthik/t:gg…

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Nice photoset from @SpotOnLondon. So many familiar faces.

is.gd/vAZocF (working link this time).

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@gangleton haha. I’m surprised that any fellows are up this early after last night.

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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

via Twitter Web Client (retweeted on 9:38 AM, Nov 17th, 2012 via Tweetbot for iOS)

tomezard 2 yr with the excellent @arpatoz in Zurich linking phenotypes to population dynamics goo.gl/xNhzv

via Twitter Web Client (retweeted on 9:38 AM, Nov 17th, 2012 via Tweetbot for iOS)

mfenner Did a little more work on our to create RSS/Atom feed for publications in your @ORCID_Org profile, e.g. sciencecard.org/easternblot.at…

via Twitter for Mac (retweeted on 9:33 AM, Nov 17th, 2012 via Tweetbot for iOS)

@yoavram @hadleywickham I’d skip 8 and the appendices. There are also many helper packages now that do positioning, themes etc.

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@yoavram @hadleywickham no. The last 1/3 of the book is outdated IMO. Early chapters are still very much applicable.

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@mbeisen I’ll keep a lookout. I live right above Cordonices park.

via Tweetbot for iOS in reply to mbeisen

@gangleton congrats to you and the other fellows. /raises glass.

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@edyong209 No no no. @labroides doesn’t speak for all of us. We’re still up, yo.

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Nerd sad that I cannot run any more simulations on a Fri night because 95% of all cores are in use.

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@yoavram @hadleywickham ggplot2 has undergone lots of changes since then. e.g. opts has been deprecated. + many other changes.

via Tweetbot for Mac in reply to yoavram

@datatelling ah. Well, before you leave sf and move away for your new gig, we should grab a drink sometime.

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silentbicycle “At this hour, I’m more interested in a restful IPA than a RESTful API.”

via Twitter for Mac (retweeted on 5:16 PM, Nov 16th, 2012 via Tweetbot for Mac)

nmatasci Last chance to apply to the this January at @iPlantCollab in Tucson. iplantcollaborative.org/learn/news/201…

via Twitter Web Client (retweeted on 4:58 PM, Nov 16th, 2012 via Tweetbot for Mac)

@hadleywickham @github agreed. I think github is missing out on the very large pool of scientists.

via Tweetbot for Mac in reply to hadleywickham

@distribecology @recology_ Good point. MD is easy to teach with no background. knitr requires some fluency.

via TweetDeck in reply to emhrt_

@recology_ @distribecology I’d vote 2. Git/version ctr/collaboration as 1. Then literature programming for pubs/other docs as the other.

via TweetDeck in reply to sckottie

@revodavid Perfect! Thanks very much, David!

via TweetDeck in reply to revodavid

@hylopsar neat, thanks! I’ll check it out.

via TweetDeck in reply to hylopsar

@revodavid Do you know of any citable sources supporting the fact that R is one of the most widely used analysis tools in academia?

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So much fail whale at my end today.

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@labroides stop oncoming traffic, hug sloth tightly, reattach sloth to nearest tree.

via Tweetbot for iOS in reply to labroides

revodavid On average, programs in R are 2x shorter than Python and 4x shorter than C++. Mathematica code is shortest. bit.ly/RZfilt

via TweetDeck (retweeted on 11:29 AM, Nov 16th, 2012 via Tweetbot for iOS)

@cboettig @omearabrian @rOpenSci @eol awesome! Twitter makes it easy to spot these things early on.

via TweetDeck in reply to cboettig

altmetric Foggy with a risk of mathematics: altmetric.com/blog/interacti… more equations = less citations?

via Twitter Web Client (retweeted on 9:07 AM, Nov 16th, 2012 via Tweetbot for iOS)

@ficaryl Here’s a better attempt at explaining the nonsense ;)
theatlanticwire.com/topics/horse-e…

via TweetDeck in reply to ficaryl

@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/…

via TweetDeck in reply to ficaryl

@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,

via TweetDeck in reply to vitoaguiar

@larysar thanks, that’s the most reasonable solution short of mailing a hd.

via TweetDeck in reply to larysar

@labroides sure thing. Just paying it forward.

via Tweetbot for iOS in reply to labroides

What is the easiest way to transfer 150 gigs of data to a collaborator? Too big for Dropbox. DVDs in the mail?

via Tweetbot for iOS

@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.

via Tweetbot for iOS in reply to labroides

@ficaryl the juxtaposition of words makes it read a bit like @Horse_ebooks

via Tweetbot for iOS in reply to ficaryl

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