Archive for June, 2010

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Summer update #1

June 23, 2010

It has been a little while since I last blogged. I have been busy finishing up a Ph.D. related project, namely my written prelim, and haven’t had any time for posting updates. However, I have three important things.

First, I am continuing to work with the Fedora project to get JAGS formally into Fedora. Afterwards, I do hope to get R-rjags and R-coda into Fedora as well but these are much more easily installable via the fantastic R package manager and admittedly are very low on my priorities.

The second big thing that I’ve been working on is writing a KDE/Qt R editor. I know cantor and rkward exist and that you can use kate, kwrite, etc., however, none of these editors really meet my R needs. Rkward is the closest, but is way too feature rich for my needs. I am hoping that my R editor will be similar to ESS and TINN-R. I mostly just want syntax highlighting (which I already have partially implemented), the ability to easily send a line(s) of coding to a terminal using a keystroke (will default to Ctrl+R like RGui in Windows but will be configurable in a preferences dialog), the ability to launch R from the editor in a separate window (e.g. konsole, gnome-terminal, etc.), and the ability to run Sweave on the document. Maybe by the end of the summer I will be ready to release a preview or a beta version, but I am not sure.

Finally, and lowest down on the priority list, I plan on writing a MCMC program in C++. After creating this program and bolstering my C++ and MCMC skills, I will stop writing the program once I’ve learned enough (as it’s a didactic experience) and instead will actively contribute to JAGS or MCMCglmm or some other Bayesian program that can interact with R. Alternatively, I might consider trying to create a KDE/Qt frontend to JAGS that could also call R and rjags just to run the JAGS engine and nothing else. I am uninterested in a Qt fronted to R (btw, that’s called rkward).

But that’s a long way down the road.

Thoughts? Ideas? Comments?

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JAGS, rjags, and coda packages for Fedora 13 i386 & 64 bit

June 4, 2010

I spent the morning working on writing up a RPM spec file to package and maintain JAGS in Fedora. So hopefully my spec file looks good and my RPM can promptly be included in Fedora (hopefully 13). The beauty of this is that after installing JAGS from my RPM you don’t need to tell rjags where to look for JAGS because it’s already in a place where rjags will look by default. Also you don’t have to compile JAGS.

For the time being I am hosting the RPMs for jags i386 and jags 64 bit and jags-devel i386 and jags-devel 64 bit on Dropbox. Once they are accepted into Fedora they will be removed from Dropbox.

EDIT: This afternoon I packaged up rjags and coda for Fedora (also submitted for review). I hope to start maintaining these in Fedora. If you want to use them and try them out click here for rjags 64 bit and here for coda (both i386 and 64 bit) . Coda is platform independent but rjags is for 64 bit only. If you want to install rjags and you’re on a i386, just install the two JAGS rpms (jags and jags-devel) from above and fire up R and run:
install.packages("rjags")

And that should be it.