Matthew Hoffman and Andrew Gelman have posted a paper on arXiv entitled “The No-U-Turn Sampler: Adaptively Setting Path Lengths in Hamiltonian Monte Carlo” and developing an improvement on the Hamiltonian Monte Carlo algorithm called NUTS (!). Here is the abstract: Hamiltonian Monte Carlo (HMC) is a Markov chain Monte Carlo (MCMC) ... [Read more...]
The French agronomy research institute INRA is organising a Fall school in La Rochelle, Nov. 28 – Dec. 02, on Bayesian methods, oriented towards the applications in food sciences, environmental sciences, and biology. The provisional program (in French) is ■ Initiation aux outils informatiques R et WinBUGS (TP et réalisation de projets sur ... [Read more...]
Nothing related with programming, I am afraid! Just a few bugs visiting my passion vine…
I find the green bugs quite interesting with their back “engravings”, even though they are most likely pests …
Filed under: pictures, ...
I posted a question to the R-Mixed-Model mailing list but have not had any responses yet:--------------------------------------------------------------------------------------- Dear All,I wonder if anybody has tried to make glmmBUGS work with JAGS. Mya...
I have an entry here about how to install JAGS and rjags in Fedora. However, I have exchanged emails with Robert Dorazio and Dr. Martyn Plummer. Here are the easier steps to compile JAGS and install rjags in R.
1. After you extract the source code... [Read more...]
Christopher has the RPMs (for Fedora users) for JAGS, coda, and rjags on his blog. The specific blog entry is here:
If you have trouble installing JAGS or rjags in Fedora,... [Read more...]
Do not resort to Monte Carlo methods unnecessarily. When I received this 2009 Springer-Verlag book, Computational Statistics, by James Gentle a while ago, I briefly took a look at the table of contents and decided to have a better look later… Now that I have gone through the whole book, I ...
Glancing perchance at the back of my Amstat News, I was intrigued by the SAS advertisement Bayesian Methods Specify Bayesian analysis for ANOVA, logistic regression, Poisson regression, accelerated failure time models and Cox regression through the GENMOD, LIFEREG and PHREG procedures. Analyze a wider variety of models with the MCMC ...
In our department and various places on the Intertubes, SAS programmers set the HTML title tag (which sets the title in web browsers and on search engines) in ODS using the headtext option: ods html headtext="My great report" /* wrong! */ file="foo.html"; This may work in some situations, but ... [Read more...]
After installing Weka/RWeka in R, you may get this error if you try to load RWeka in the same session: require(RWeka) Cannot create Java virtual machine (-4) Error : .onLoad failed in 'loadNamespace' for 'RWeka' Solution: Just close R and re-open it. Cause: Apparently the installation requires some initialization. ... [Read more...]
Recently Microsoft Office Outlook 2007 started giving me the vague error message Outlook cannot open this item. The item may be damaged. The message would appear randomly throughout the day. Sometimes five error message boxes would be stacked up on top of each other. OK, but which item? What kind of ... [Read more...]
I have got emails occasionally from JAGS users, asking about our new R package: R2jags. Basically, R2jags runs JAGS via R and makes postanalysis easier to be done in R. Taking advantage of the functions provided by JAGS, rjags a... [Read more...]
Just when I am about to convert myself into a Linux user, I found this. Running R in the command mode in the Window system is much faster. Here is a simple test:in the Window interface:__ system.time(rnorm(1000000)%*%rnorm(1000000)) user system elapsed 1.06 0.05 1.14 in the command mode__ system.time(... [Read more...]
JAGS was developed to help those non-Window users to be able to use BUGS. However, I found it is very hard to install JAGS and its R package-rjags. Here is my note on how to install JAGS and rjags in Fedora 10. The note here should work for all Linu... [Read more...]
I have wrote about my experience with jags here. Martyn Plummer has updated jags recently and now jags can get as he claimed. Jags is fast and its source code is more manipulable (It's written in C++).I and Masanao wrote a package, R2jags, for runnin... [Read more...]
JAGS is a cross platform BUGS. Because it runs in a command mode, it is somewhat faster than other BUGS. However, I found it is a bit tacky to use it as a Windows/PC user. I found the manual very useful but some of the language is a bit ... [Read more...]
I coauthor a paper with Ozan, a friend who I know when I was TAing Bayesian Methods in ICPSR. The paper tries to see if the 9/11 has any effect on American's attitudes on Muslim. We have dataset from different years: 2 from pre-9/11 periods and 2 from ... [Read more...]
I used to fit Bayesian model using WinBUGS via R a lot. But now I am more and more prone to run models on OpenBUGS directly. I have document the reason why I like OpenBUGS and wrote a auto OpenBUGS function here. In short, I like to be able to ... [Read more...]