In response to a comment by Emmanuel Charpentier, I should write a few words about what has changed in JAGS 3.3.0.
JAGS 3.3.0 is released
The source tar ball and Windows installer for JAGS 3.3.0 are now available from Sourceforge. Binary packages for other platforms should be available shortly: see the JAGS homepage for details of how to get hold of a binary version for your platform.
Bad Graphs
In May we published an article on the burden of cancer attributable to infection in The Lancet Oncology. On the left is Figure 2 from the article, which shows that the majority of the burden is attributable to just four infectious agents. Continue reading
Online courses
Back in December I wrote about the online machine learning course from Stanford, and how I was looking forward to the course on probabilistic graphical models (PGMs). Unfortunately the second course did not work out so well for me, despite my obvious interest in the topic, and I never completed it. The workload was simply too intense and the weekly deadlines were incompatible with my busy travel schedule during the springtime.
The Stanford courses are now part of an umbrella organization called Coursera, which is aggregating online courses from Universities all over the world. This 20-minute TED talk by Daphne Koller, co-founder of Coursera and lecturer on the PGM course, explains Coursera’s social mission. I now realise I am not really part of the target audience. In fact Coursera has its eye on the global marketplace for education. By removing financial and logistic barriers to entry they aim to make higher education accessible to people who would never otherwise have a chance to follow such courses.
An interesting point made by Koller is that online courses generate large amounts of data, which can be analyzed to improve the course the next time it is repeated. The same idea is reiterated by Peter Norvig in a 6-minute TED talk. Norvig’s talk also explains why the weekly deadlines – which I complained about above – are necessary to make these courses work.
Not discouraged by my failure on the PGM course, I have signed up for two autumn courses: Heterogeneous Parallel Programming and Functional Programming Principles in Scala. Both are relatively short (6 and 7 weeks respectively) so should be more manageable although I am sure I will have to give up one of them.
Stan
Andrew Gelman has announced the release of Stan version 1.0.0 and its R interface RStan. Stan – named after Stanislaw Ulam, the inventor of the Monte Carlo method – is a new MCMC program that represents a major technological leap forward. It works flawlessly on my Linux desktop and is very, very fast. (Note that I have nothing to do with the Stan project: I am just posting this here because it is clearly of interest to JAGS users). Continue reading
Lack of reproducibility in the glm module
Kodi Arfer sent a script that reveals a bug in the glm module. If you set the random number generator seed in the initial values, then the output from jags should be identical every time you run the model. Unfortunately, Kodi’s script shows that this is not the case. In the interests of transparency I am putting a note here on the blog but I currently have no idea how to fix this.
The script, and some sample output, is below
Continue reading
Course: Statistical Practice in Epidemiology with R
Statistical Practice in Epidemiology with R is a one week course aimed at promoting the use of R among epidemiologists. This annual course has been running almost every year since 2004. Last year it took place in Lyon, France, but is now returning to its spiritual home in Estonia. The course will take place from 25 to 30 May 2012 at the Strand Hotel in the seaside resort town of Pärnu.
For more details about the course, including how to apply, see the SPE home page. The deadline for applications is April 1 2012.
