This took somewhat longer than planned. Due to the long lapse between JAGS 3.4.0 and JAGS 4.0.0 there will be quite a long beta period. I shall explain some of the important changes in a series of follow-up posts.
I cannot currently upload the files to Sourceforge. They are still recovering from a major outage from a couple of weeks ago. For now, you can download the source tar balls for JAGS-4.0.0 beta and the R package rjags_4-1 from my Google Drive. (Click the icon and then the download symbol that appears in the black bar at the top of the screen).
If you want to want to work with R and JAGS on a hard multivariate measurement error problem in nutritional epidemiology, then take a look at this advert.
IARC is based in Lyon, France. For informal queries approach me or my colleague Pietro Ferrari who is the PI on this project.
I returned from my Christmas vacation to find an unexpected gift had arrived: a mug illustrating Bayes theorem with dogs.
The Longjing tea was a gift from my boss.
The was a bit of a mystery until John K Krusche revealed himself as the sender. The image is from the cover of his book Doing Bayesian Data Analysis: A Tutorial with R, JAGS, and Stan, now in it’s second edition.
I have been investigating the use of the Intel Math Kernel Library (MKL) and Intel compilers to produce R binaries on Linux, and have included some benchmarks to compare these with GNU compilers and the reference BLAS and LAPACK. I am making my notes public, as the topic may be of interest to others. Bear in mind that this is a work in progress: R-intel-fedora
This is a quick update to yesterday’s post on polling for the referendum on the independence of Scotland from the UK. The final result is 55.3% for No (i.e. staying in the union), 44.7% for Yes. This is consistent with the opinion polls, which predicted a win for No, but the margin is certainly bigger than predicted by the opinion polls, especially in the run-up to the referendum.
The image below from whatscotlandthinks.org shows a “poll of polls” – a running mean of opinion polls – which is a smoothed version of the figure I showed yesterday. The average of the last 6 polls on the day before the referendum gave a prediction of 52% for Yes – only a 4 percentage point difference compared with the 11 point difference seen in the referendum. This vindicates Stephen Fisher’s analysis showing that opinion polls tend to overestimate the desire for constitutional change.
If you ignore the narrowing in the gap that apparently occurred in the last two weeks, the polls seemed to give a pretty good prediction from April to August. So perhaps this wasn’t a last minute surge for Yes, but a “patriotic spiral of silence” from No voters, as Martin Boon suggested. But I’ll leave that question to the psephologists.
The people of Scotland are voting today in a referendum to decide whether Scotland should become an independent country (“Yes”) or remain in the United Kingdom (“No”), ending the 300 year old Treaty of Union. As shown by the poll tracker above (from the website whatscotlandthinks.org) opinion polls have consistently put the No vote ahead of Yes. In recent weeks the gap has narrowed but only two polls have put the Yes vote ahead. It looks like a narrow win for No, but can the polls be trusted? Continue reading
Thanks to Matt Denwood, we now have a binary distribution of JAGS 3.4.0 for Mac OS X Mavericks. There is a separate binary for older Mac OS X releases (Snow Leopard, Lion, Mountain Lion). Both binary packages can be downloaded from the files page.
[Update 2014-09-11] The rjags package for Mavericks is now available from CRAN. To make it work, you need to have the right combination of R and JAGS:
- If you installed the R-3.1.1-mavericks.pkg version of R then you need to install JAGS-Mavericks-3.4.0.dmg
- If you installed the R-3.1.1-snowleopard.pkg version of R then you need to install JAGS-SnowLeopard-3.4.0.dmg
If you get an error about a missing symbol then you have the wrong combination of R and JAGS.
[Update 2014-11-28] Note that if you are running Mavericks or Yosemite then you cannot assume that you are running the “Mavericks” version of R, as the “Snow Leopard” version also runs on the latest releases of Mac OS X. If you are not sure which R binary package is installed then type
at the R prompt (note the dot at the beginning). This will either say mac.binary or mac.binary.mavericks. Follow the corresponding link to get the right binary version of JAGS to match your R installation.
If you are still having problems, come to the JAGS forums.