Revolutions

In case you missed it: July roundup

In case you missed them, here are some articles from last month of particular interest to R users.

This post announced a directory of R user groups available on the Revolutions blog.

This post noted that the Society of Actuaries promotes R with a regular column.

This post noted that the New York Times mentioned R in the context of SPSS's sale to IBM (as did several other media outlets).

This post offered a review of the BioConductor 2009 conference, and linked to my slides on parallel programming with R.

This post linked to the "Rosetta Code" site, where you can see standard computing problems solved in many languages, including R.

This post linked to John D Cook's tip-sheet for programmers of other languages learning R.

This post contended that working with interesting data -- like the top 100 song list -- is a good way to learn R.

This post noted that R had a significant presence at the open-source conference OSCON this year, and linked to slides of R presentations.

This post linked to an example of web-scraping using R and Rcurl.

This post provides some examples of using iterators in R.

This post noted that Forbes has identified R as an open-source venture "worth watching".

This post links to an O'Reilly interview with REvolution's Danese Cooper, talking about Open Government and R.

This post showed how one website is using R to improve performance through analysis of DNS lookup times.

This post offered a review of the UseR! 2009 conference overall, and this one discussed some of the presentations.

This post prompted a discussion about solving the Knapsack Problem in R.

This post pointed to the Learning R blog, where a comparison of ggplot2 and lattice graphics is ongoing.

This plot noted that presentations from the Rmetrics financial conference are available for download.

This plot noted another instance of R being used at Google (for boxplots).

Other non-R-specific stories in July covered power-law distributions, temporal illusions, game theory, commercial open-source, the Netflix prize, and ferrofluid. The R Community Calendar has also been updated.

Thanks to everyone who provided comments and tips and please keep them coming to david@revolution-computing.com.

The Crow Paradox

Although we can't tell individual crows apart (even experienced crow handlers have trouble), crows are capable of identifying individual humans. They do it by recognizing faces, as revealed by a clever experiment conducted at the University of Washington. This NPR video explains.

NPR: The Crow Paradox

R and REvolution Computing in the news

With all the recent activity around the various conferences, REvolution Computing has had a few mentions in news outlets recently. A quick recap:

• Following its field report from OSCON, open-source news site OStatic posted this article: The "R" Statistical Environment, and REvolution Computing, Spread Out
• James Governer, industry analyst at RedMonk, reviewed the analytics marketplace in the context of the SPSS sale with mentions of R and REvolution Computing: IBM Buys SPSS: More Quants For a Smarter Planet
• In its article on the announcement of Open Source for America, ZDNet UK mentioned REvolution Computing amongst the companies affiliated with the founders: Coalition seeks US gov't support for open source
• Cnet News had a similar article: Open-source allies woo U.S. government 
• GenomeWeb previewed the BioConductor conference and our lab session in the article Is Your R Parallel? 

R itself garnered quite a bit of media coverage recently too, especially around the SPSS acquisition, in articles in InformationWeek, Intelligent Enterprise, Seeking Alpha, in OSCON reviews by Ted Leung and Dan Meyer, and in the New York Times.

Belated thoughts on DSC 2009

John Maindonald has just posted a great collection of notes about his experiences at the two recent R conferences in Europe, UseR! and DSC. Especially if you weren't able to attend, his notes give a great sense of the atmosphere and focus areas of the two conferences.

It also reminds me that I hadn't yet posted my own thoughts about the DSC conference in Copenhagen. I've just returned home from all my conference travels (sadly, I can't make JSM) and am just now tying up some loose ends. So let me correct that omission.

For those that haven't attended before, DSC is quite a different conference than UseR. Unlike UseR which is focused on how R is used, DSC is focused mainly on R itself: how it works, and how it can be improved. DSC is also quite a bit smaller: about 60 attendees compared to almost 500 for UseR. But that's also its great strength, providing an intimate and social atmosphere to get to know the people behind R, and to have in-depth discussions about R and its place in the open-source, programming, and statistical world.

The format of the conference also allows for some deeper explorations into R issues. Save the opening talk (this year, an excellent history of computing from Tue Tjur), all talks are contributed, and all are 35 minutes in length (compared to 15 minutes for a contributed UseR talk). There are also few parallel sessions, meaning that it's easy to see all the talks you're interested in.

Some of the most memorable talks for me were:

• John Chambers talking about the background and motivations of the S3 and S4 class systems in R -- with some suggestions of future developments from the audience
• Deepayan Sarkar and Michael Lawrence talking about a new, faster graphics subsystem linking to Qt for interactive graphics
• Uwe Ligges, giving insight to some of the practical implications of how CRAN checks submitted packages 
• Karim Chine demonstrating how the Biocep front-end can use remote R sessions transparently, including R running on Amazon EC2 
• Nicholas Lewin-Koh discussing a real-life success story at Genentech, delivering statistical applications to scientists (but not R users) with Rserve
• Doug Bates talking about some of the slick computational internals of the lme4 package, making R the only package able to fit mixed models with very large numbers of parameters 
• Stefan Theußl describing the workings of R-Forge, now the development repository and build tool for hundreds of R projects
• Simon Urbanek demonstrating iPlots Extreme, an amazingly fast and beautiful linked-graphics system coming soon for R 
• and Hadley Wickham, discarding his planned talk in the wee hours of the morning to propose a new way of thinking about object-oriented programming in R and prompt some fascinating discussion from the audience. 

My own talk was on a new Integrated Development Environment (IDE) for R that the REvolution Computing is sponsoring and developing. I talked about the forthcoming changes to R (mainly by Robert Gentleman and Duncan Murdoch) that will allow step-debugging of R code from the command-line, how REvolution Computing's developers are integrating these features into Microsoft's Visual Studio Shell. My slides are available for download (1.3Mb PDF). There will also be a proceedings volume from all the talks published next year.

All in all, it was a great conference -- congratulations to the organizers (and not least for such a wonderful conference dinner!). I look forward to the next meeting in 2011.

Package Update Roundup: Jul 2009

This is a list of new or updated packages that were released for R in July, as announced on the r-packages mailing list. To include other updates on this list, please email David Smith. For a complete list of all updates on CRAN, see the CRANberries archive for July 2009. Follow package name links for ratings and other information on crantastic.org.

dlmn, a new package for distributed lag nonlinear models, was released.

doMC, a parallel backend for the foreach package based on multicore, was released.

exact2x2, a new package for exact conditional tests for 2x2 tables, was released.

foreach, a new package for simple, scalable parallel programming, was released.

iterators, a package implementing iterator constructs, was updated to fix a bug affecting certain locales.

plotrix, a package of various plotting functions, has been updated to improve performance.

sculpt3d, a new toolbar GUI for brushing RGL plots, was released.

SweaveListingUtils, a package of utilities to create TeX markup for use with Sweave, was updated (in April, but not previously announced).

tikzDevice, a new graphics device for LaTeX-ready output from R graphics functions, was released as a beta version.

tsDyn, a package for time series analysis based on dynamical systems theory, was updated with enhanced functionality for threshold autoregression models.

CRAN mirrors, mapped

Packages and sources for R are distributed and hosted at a network of volunteer-run FTP sites, collectively known as CRAN mirrors. There are currently 69 CRAN mirrors worldwide, and the CRAN statistics page helps you find one that's working. But you'll get better performance when downloading packages -- and help share the load -- if you choose a geographically local mirror.

Barry Rowlingson has created a couple of tools to help you do just that. The first is Cranography, an interactive map showing all of the CRAN mirrors around the world. Barry used the geocode geonames package to determine the locations of the mirrors (with some manual adjustments), and the map itself was built using OpenLayers. Click on the screenshot below to try it out.

So that's how you can find the closest CRAN mirror, but is it the fastest? Barry offers a solution there, too: the cranometer function. It estimates the speed of each CRAN mirror by measuring the time it takes to download the NEWS file. It's a rough-and-ready estimator (be sure to check the caveats) but it's certainly an interesting application of the internet-capable functions in R.

Barry Rowlingson: Cranography