I’ve been learning Ruby, and decided to scratch an itch: getting citations for papers to put in a bibtex file or my Zotero library. This usually requires two parts: 1) searching for an article with keywords, and then 2) getting the citation once the paper is found. Since I am lazy, I would prefer to do this from the command line instead of opening up a browser. Thus => cites. (Note, I’m sure someone has created something better - the point is I’m learnin’ me some Ruby) cites does two things: ...

Gaug.es is a really nice looking analytics platform as an alternative to Google Analytics. It is a paid service, but not that expensive really. We’ve made an R package to interact with the Gaug.es API called rgauges. Find it on Github and on CRAN. Although working with the Gaug.es API is nice and easy, they don’t keep hourly visit stats and provide those via the API, so that you have to continually collect them yourself if you want them. That’s what I have done for my own website. ...

I started using Jekyll when I didn’t really know HTML, CSS, or Ruby - so I’ve had to learn a lot - but using Jekyll has been a great learning experience for all those languages. I’ve tried to boil down steps to building a Jekyll site or blog to the minimal steps: Install Jekyll Mac/Linux/Unix: Install dependencies: Ruby RubyGems Install Jekyll using RubyGems gem install jekyll (you may need to do sudo...) If you’re having trouble installing, see the troubleshooting page. Windows: Jekyll doesn’t officially support installation on Windows - follow these steps for a Windows install. ...

Code in journals, that is, code you would type to do some programmatic operation in say R or Python, is kind of a mess to say the least. Okay, so you can SEE code in papers, but code is not formatted in a way that facilites reuse. If an author in a paper writes out some code for software they create, or an analysis they do in the paper, wouldn’t it be nice for a reader to be able to copy and paste that code directly into whatever environment that code should execute in, and actually work. Of course there is dependencies, etc. for that software to worry about, but here I am just concerned with the code formatting in articles. Code is displayed as an image in some cases (gasp!). Additionally, there’s this thing called the internet, and we can use color, so let’s highlight code already. At least in one of our recent rOpenSci papers in F1000 Research, they do use syntax highlighting - w00t! ...

Note: This is cross-posted from the rOpenSci blog, which will update with this post when our technical snafu is fixed. With the US government shut down, many of the federal government provided data APIs are down. We write R packages to interact with many of these APIs. We have been tweeting about what APIs that are down related to R pacakges we make, but we thought we would write up a proper blog post on the issue. ...

Eduard Szöcs and I started developing a taxonomic toolbelt for the R language a while back , which lets you interact with a multitude of taxonomic databases on the web. We have a paper in F1000Research if you want to find out more (see here). I thought it would be fun to rewrite some of taxize in other languages to learn more languages. Ruby and Python made the most sense to try. I did try others (Julia, Node), but gave up on those for now. The goal here isn’t to port taxize to Python and Ruby right now - it’s for me to learn myself some coding. ...

I am on my way out of academia, so I want to share what I won’t ever get around to finishing. I started a paper many years ago examining the prevalence of natural enemy pressure on pollinators, and patterns of occurrence of pollinator natural enemies in relation to plant attributes. Anyway, Figshare seemed like the perfect place to put this. I licensed the materials under CC0, so feel free to do whatever you want with it. Check it out at https://figshare.com/articles/dataset/Pollinator_niche_breadth_and_natural_enemies/803123 ...

I started an R package a while back, and a few people have shown interest, so I thought it was time to revist the code. govdat is an interface to various APIs for government data: currently the Sunlight Labs APIs, and the New York Times congress API. Returned objects from functions are simple lists. In future versions of govdat, I may change how data is returned. The following are examples (which is also the package vignette) of using the Sunlight Labs API. I will add examples of using the New York Times Congress API once their site is up again; I’m doing this on 2013-08-28, just after the takedown of their site. ...

ScienceOnline Climate I recently attended ScienceOnline Climate, a conference in Washington, D.C. at AAAS offices. You may have heard of the ScienceOnline annual meeting in North Carolina - this was one of their topical meetings focused on Climate Change. Another one is coming up in October, ScienceOnline Oceans. Search Twitter for #scioClimate (or the entire list of hashtags here) for tweets from the conference. One of the sessions I attended was focused on how to democratize climate change knowledge, moderated by a fellow from the Union of Concerned Scientists. Search Twitter for #sciodemocracy to see the conversation from that session. There was a lot of very interesting discussion. ...

I recently attended ScienceOnline Climate, a conference in Washington, D.C. at AAAS. You may have heard of the ScienceOnline annual meeting in North Carolina - this was one of their topical meetings focused on Climate Change. I moderated a session on working with data from the web in R, focusing on climate data. Search Twitter for #scioClimate for tweets from the conference, and #sciordata for tweets from the session I ran. The following is an abbreviated demo of what I did in the workshop showing some of what you can do with climate data in R using our packages. ...