XKCD is so me and my coding

(by Christina Pikas) Apr 17 2015

Check out the alt text on the original site.

XKCD cartoon from: http://xkcd.com/1513/

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Straddling the fan-girl critical thinker divide, while trying not to be not-even-wrong

(by Christina Pikas) Apr 12 2015

Working on the tougher bits of my dissertation now (defense is really scheduled, finally), and trying to come to terms with my relationship with the science blogosphere and twitterverse (or whatever). Some other articles - and one was particularly cringeworthy - on the topic have been in the not-even-wrong category. It's like someone trying to explain your culture to you and just getting it wrong (like my old boss who kept insisting I was Orthodox even though I told her a million times I'm Catholic, just Eastern Rite/Ukrainian).

Am I in a privileged position here on Scientopia? To have attended Science Online for several years? To have met and chatted with many science bloggers? Thought deeply about science blogging since about 2004?

Am I just a fan girl who gushes about the wonders of blogging to anyone who will listen? Despite being told that it's dead? (at least people have finally stopped telling me wikis will take over. siiiiiigh). Am I uncritical in my support?

If I am in a privileged position as a long time (peripheral?) participant observer, how do I convey that? These other articles - I can often see how they got to the results and interpretations they did, but meh.  Maybe I'm fooling myself, too, but in a different way? they are published, I am not.

So looking at definitions of prolonged engagement and persistent observation and well, damn, I had better go to bed as a) Easter tomorrow and b) twin 3 year olds get up when they want to.

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Why FriendFeed Rocked

(by Christina Pikas) Apr 10 2015

If you're a librarian or into open access or scholarly communication, at some point you've probably heard of FriendFeed. The service closed today after seven years and it was kind of like the final episode of Cheers or MASH. It had been acquired by Facebook a while ago and development had stopped. Reliability was down. The number of active users was down and had never been anywhere near Facebook even in its prime. There was no way for it to make money - no ads, no premium features, no subscriptions.

With that said, there are a lot of people who are really torn up about them shutting it down. We built a community there - a stay at home mum from Australia, an engineer from Detroit, a software developer from Alberta, several ministers, lots of other neat people, and the LSW. The Library Society of the World is sort of an anti-association. Read Walt's discussion of that in his May 2015 Cites and Insights (pdf)

So why did it work? When I started with it, there were lots of social software things all over - blogs, Twitter, Flickr, del.icio.us... and there were more and more as time went on. Many of these act like they will be your one and only place. But that's obviously not true. They have different functions, different communities, different affordances... Used to be you could share things from your Google Reader account but that wasn't the same.

What FriendFeed did is to bring all of these feeds in to one place, with a little snippet or picture, and let you comment and reshare and like. You could share something right there, but you didn't have to. It would try to group things if you had your blog posting directly and your Twitter stream duplicated that. You could see what your friends liked and find new and interesting people that way. For the first few years I was on there I was only going to follow library people, well, and of course Heather, and Cameron, and Neil, and Egon, and ... but I was glad I did get to enjoy and eventually follow some really neat people.

If someone posted something you didn't want to see, you could hide just that post, or you could hide things they shared via a particular feed. You could block someone completely so you wouldn't have to see their comments.

I've played with a lot of other tools, but FriendFeed just worked for me.  It was a great source of recipes, if nothing else!

There was a team of savvy folks archiving as much as they could. So far, the best way to see what it was like is to see Micah Wittman's FriendFeedmemorial.com . That's really pretty cool.

So where is LSW now? We're trying Discourse at thelsw.org (doesn't allow you to bring feeds in but you can get a cod badge). We're also trying http://www.frenf.it which is really, really cool... but we don't know how sustainable. And we followed each other on Twitter... but it's not the same.

I miss it already!

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Which are the bestest? Top articles from a diverse organization - part 1

(by Christina Pikas) Apr 01 2015

In which Christina goes into the weeds, yet not really thoroughly enough... anyhoo.

So MPOW is approaching an anniversary and we're looking at retrospectives of all sorts. What are the top articles we've published in the literature? What do you mean by top? Ok, so let's say that top means most cited - just for argument's sake. Is it really fair to compare a biomed article to an aerospace engineering article? An article published last week (ok, if in a special issue it might come complete with citations attached) with one published 5 years ago? 10? 20? Review articles with .... you see where this is going.

I had thought to normalize by 5 or 10 year periods and use the subject categories in WoS. But... 1) there are a lot of them 2) they overlap 3) argh.  And things like Acoustics, for example. JASA covers biomed like hearing stuff and it covers underwater sound... but they're not cited the same... at...all.  The acoustics category covers medical journals, physics journals, and maybe some math and engineering (I'd have to look again to be sure).

At the same time, the nice folks there on SIGMETRICS had a argument starting last weekend and going through the beginning of the week on various normalization schemes. One of the complaints against the impact factor is that it's an average and averages don't work on skewed distributions. And the WoS categories suck.

So... what I'm trying to do now is both fractional counting (and I'm checking to make sure I know what that is, but  I think you don't get credit for 1 citation you get credit for 1/(total things cited by citing article) so like a citation from a review article is worth a lot less than one from a regular article because it may be like +1/200 vs. +1/30). And then I'm normalizing by percentile. Not even normal percentile but this Hazen(1914) percentile. Tricky.

I'll be sure to share the script once I've got it. So far the method looks like:

  1. Find my org, relevant time period, articles only in WoS.
  2. Sort by cited, pull off the most cited or all the ones cited more than x or something. Save them down in plain text full record (probably don't need citations?)
  3. Then for each of the top, click on Times Cited. Export them all down in Tab del Windows UTF-8
  4. Move them over to data folder
  5. Run R script (to be shared when I'm sure it's right) to get the new TCs and stick them into the file from 2

*note: if your thingy was cited more than 500 times, you can't export them all at once. Also this would not be practical if you have someone with like thousands of citations. If you do, I would just take the plunge and call that one of the best. We only had 5 over 500.

Next, I'll put them into the ISI.exe script and then the i3 script from here.  See what happens.

As for normalizing by year. I was thinking about maybe omitting a couple of years or so and then doing 5 year bins 3 times and then doing 10 year bins. Not sure. Willing to take advice. It's a 75 year history, but there was a similar paper done in 1986 so I only agreed to go back to 1980. Before a certain time - no longer necessarily 1973 - the affiliation/address aren't there. One very nice retiree I had the pleasure to meet just died and I found that he was listed in Garfield's top cited articles. His work on polar gases is not coming up in the search so it's definitely not complete that far back.

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Another dissertation on science blogs

(by Christina Pikas) Mar 31 2015

Any readers interested in my work (and you'd probably have to be following me for a while to even know what that is), will probably be interested in that of Paige Brown Jarreau. She's a PhD Candidate at LSU and is defending any day now. She did a massive set of interviews and a survey and has shared some of her results on FigShare, on her blog, and in her Twitter stream. So far we've mostly had a glimpse of her findings - can't wait to see the rest of her dissertation (good grief the rate I'm going I guess I'll get a chance to cite it in mine :) )

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OAuth in TwitteR much easier now, whew!

(by Christina Pikas) Mar 18 2015

Not like I should be messing with this at this point, but I wanted to retrieve a tweet to provide evidence for a point. Anyway, instead of the like 50 step process in the past, you now follow the instructions in the TwitterR readme: http://cran.r-project.org/web/packages/twitteR/README.html with the exception of you now put your access token and secret in the *single command* now, too, like so:

setup_twitter_oauth(consumer_key, consumer_secret, access_token=NULL, access_secret=NULL)

Then you can just search or whatever. Wow!

Very nice. How much time did I spend playing with the old method?

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Do too - I'll show YOU!

(by Christina Pikas) Mar 15 2015

Lookin' for some lit as one does when one is supposed to be writing instead of adding to the impossible list of things to double back to add to the lit review... Via who-cited-who and Scholar, ended up on a TandF page. Looked interesting - right click, reload through proxy for my place of work. It sneers - "sorry you do not have access to this article" - access options include paying $40 for the article. Um. No.  LibX has kindly highlighted the doi... clicked... got to my beautifully customized SFX page (with Umlaut) and it's full text on a major aggregator. Take that you! Ha!

And, this is probably even better than seeing it at the publisher, because our custom FindIt page tells me the article has been cited 23 times (oh well maybe not I see that TandF does offer that info, too).

Sadly though, I'll bet hardly anyone at my place of work would have thought to take this path.

 

Edited to add: moments later looking at JSTOR. They kindly ask if I think I should have access... then let me pick my institution and do a shibboleth login et voila. (price would have been $14 without).

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Polar and Ellipsoid Graphs in iGraph in R

(by Christina Pikas) Mar 12 2015

I'm still working to do some additional graphs for the project mentioned in this earlier post. It was too crowded with the Fruchterman Reingold layout, so my customer suggested we do a circular layout with one category in the center and the remaining on the outer ring. I said sure! But when I went to do it, I found only star layout (one in the center) and ring layout. No polar layout. I tried a few things but finally broke down and asked. Quick perfect answer on StackOverflow (as often happens).

That led to this:

Polar Layout

But hey, still pretty jammed up. So what about an ellipse? Sure!

What's that equation again?

 \frac {x^2}{a^2} + \frac {y^2}{b^2} =1

 

But that's a hard way to do it when I need x and y values in a matrix. This looks better:

x = a \cos(\theta) , y=b \sin(\theta)

And this is how I did it.

ellip.layout <- function(a,b, theta) {
cbind(a*cos(theta), -b*sin(theta))
}

systems <- which(V(g)$category == "System")
comp <- which(V(g)$category != "System")

a<- ifelse(V(g)$category == "System",4,5)
b<- ifelse(V(g)$category == "System",0.5,1)

theta <- rep.int(0, vcount(g)) #creates a blank vector
theta[systems] <- (1:length(systems)-1) * 2 * pi / length(systems)
theta[comp] <- (1:length(comp)-1) * 2 * pi / length(comp)

layout<- ellip.layout(a,b,theta)

plot.igraph(g, layout=layout, asp=0)

Originally I was getting the outer ring to be a circle anyway, but then I asked the mailing list and it was a matter of setting asp (aspect ratio) to 0.

Here's where I ended up:

EllipseETA: If you do labels, there's a neat trick to make them always outside the circle. See here: https://gist.github.com/kjhealy/834774

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Post I wish I had time to write: Scientific meetings and motherhood

(by Christina Pikas) Feb 24 2015

I was reading Potnia's new post on meetings - why to go to them - and nodding my head vigorously (ouch) and connecting that to the part of the dissertation I'm writing now on tweeting meetings and the research over the years on how scientific meetings work and contribute...

and I got very sad. I'm a real extrovert and a magpie of all sorts of different kinds of research, but I can't justify spending my limited time reading articles that aren't pretty directly relevant to my job or my dissertation. When I went to bunches of meetings, I could soak a million little tidbits up, meet the people doing the work, browse lots of posters and talk to their authors. It's really a very efficient way to see what's up with a field.

and now... I haven't been to a conference since I was in my first trimester with my twins :(   Sure, I've listened in to some webinars and followed some tweets. It's not enough.

Would childcare at a venue help?  I don't know... I'd still have to get them there, I'd have to trust the childcare (what if I got there and checked them out and didn't like what I saw?), and I'm paying for childcare at home even when I go and money is super tight now with my income being the only one in our household for more than a year.  I thought about bringing my sister along and then we could see the sights together outside of hours. My work would pay my travel and my room and so I'd just have to pay her travel and everyone's food. But I can't really even swing that right now....

 

So yeah... at least there's twitter. The post I'd like to write actually cites references and what not.

And I'm only the 10 millionth person to have this issue this year so I  know I'm not a special snowflake but that doesn't mean I can't still bitch about it.

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Exporting high resolution graphs from RStudio

(by Christina Pikas) Feb 12 2015

This may not be obvious until you look into it but apparently the default export from RStudio -  if you use the nifty little tool in plots tab on the lower right hand side -  is 72dpi. This is fine for showing on web pages, typically, but is not enough for print. Particularly if you're submitting to a journal or something like that. There's lots of advice, but I found it somewhat confusing.

RStudio Interface for Windows from RStudio.com

RStudio Interface for Windows from RStudio.com

I found these posts helpful:

  • http://blog.revolutionanalytics.com/2009/01/10-tips-for-making-your-r-graphics-look-their-best.html
  • https://danieljhocking.wordpress.com/2013/03/12/high-resolution-figures-in-r/
  • http://www.r-bloggers.com/exporting-nice-plots-in-r/

I think someone I was reading just got out of RStudio and did his work in the standard interface. Really, there's no need for that. I also read somewhere that Cairo is not really used any more? There is a way to export to pdf from RStudio and check a box to use Cairo...

Here's what I did.

CairoPDF(file="something.pdf", width=11, height=8.5, family="Helvetica", pointsize=11)

set.seed(1337)

plot.igraph(g, layout=layout.fruchterman.reingold, edge.arrow.size=0.4, edge.color="black", vertex.size=V(g)$degree, vertex.label.dist=V(g)$vertex.label.dist, vertex.label.color="black", vertex.label.family="sans",edge.curved=TRUE, vertex.label.cex=V(g)$vertex.label.cex, edge.lty=E(g)$edge.lty, vertex.frame.color=V(g)$frame.color)

dev.off()

A couple of notes:

  • I found I needed to increase the arrowhead size
  • I needed to decrease the font size
  • I needed to set a seed so I was only changing one thing at a time as I experimented
  • When I did png, my dotted lines didn't look so dotted anymore. I didn't feel like messing with that further


Cairo(file="something.png", type="png", units="in", width=10, height=7, pointsize=12, dpi=300)

set.seed(1337)

plot.igraph(g, layout=layout.fruchterman.reingold, edge.arrow.size=0.1, edge.color="black", vertex.size=V(g)$degree, vertex.label.dist=V(g)$vertex.label.dist, vertex.label.color="black", vertex.label.family="sans",edge.curved=TRUE, vertex.label.cex=V(g)$vertex.label.cex, edge.lty=E(g)$edge.lty, vertex.frame.color=V(g)$frame.color)

dev.off()

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