Friday, May 21, 2010

Bayesian disease mapping

Here is a slide showing how to make R to extract results from WinBUGS and show them in maps.

Thursday, May 20, 2010

Sunday, May 16, 2010

Bayesian change point analysis

Here is an example using MCMCpack. The same model can be done with WinBUGS (and thus JAGS), as demonstrated in "Bayesian Computation with R".

Sunday, May 09, 2010

Emacs and screen

This post explains how to get Emacs works with the "screen" command.

Sweave with Emacs and ESS, problem solved!

With help from Seb, the nagging problem I had when trying to sweaving with Emacs and ESS ( has been solved.

First of all, apply the patch for ess-swv.el, provided by Seb. Second, set the default pdf viewer for ESS by "C-h v ess-pdf-viewer-pref ", then change the value from "nill" to "evince". Now I can directly sweave my Rnw document by pressing "M-n s", and see the pdf output by pressing "M-s P".

It has been a quite pleasant experience interacting with free software developer/maintainer.

By the way, Emacs 23.2 just got out, and it looks great on my Ubuntu box (the font scale problem that comes with the proprietary Nvidia driver is gone).

Friday, May 07, 2010

OpenOffice quick-starter caused Ubuntu unable to shutdown?

According to this post, the shutdown problem on Ubuntu 10.04 was caused by the Openoffice quick-starter program. Once the program is closed, the problem goes away. So strange.

Thursday, May 06, 2010

Problem with the proprietary Nvidia driver

The reason why my ubuntu 10.04 box cannot shutdown is the proprietary nvidia driver. I learned this the hard way: I backed up all my data and wiped out my existing installation and installed a fresh new copy, and experimented step by step. I was able to replicate the problem when I enabled the proprietary driver, and the problem when away when I disabled it.

Although I cannot enable the desktop effects, at least I have a stable and efficient computational environment now.

-------------------------------- May 8 ----------------------------------------------

This is not true. The problem with shutdown is caused by OpenOffice quick starter program, not the proprietary Nvidia driver. After enabling the driver, 1) boot-up time increased from 20s to 25s, 2) Emacs fonts increased several fold.

Wednesday, May 05, 2010

Monday, May 03, 2010

Compile aML with GCC 4.4.3 (64-bit)

I was able to successfully compile aML with GCC 4.4.3, which is part of Ubuntu 10.04. I only need to make changes on two files to avoid warning messages: "encrypt.f" (replacing "data str95/'Y,h=(ufSBF&H6W!LZ|boq1yJsX^Ax+K3U5r[mDlNOg7jn;-V:z]k/e *)v#2GQC$t''{c\\">%@~w?8dMREiT0a*9}<`\\._4PIp'/" with "data str95/'Y,h=(ufSBF&H6W!LZ|boq1yJsX^Ax+K3U5r[mDlNOg7jn;-V:z]k/e *)v#2GQC$t''{c\">%@~w?8dMREiT0a*9}<`\._4PIp'/") and "getdatainfo.f" (replacing "data backslash/'\\'/" with "data backslash/'\'/")

Sunday, May 02, 2010

Making Ubuntu boot in 19 seconds

Some serious Ubuntu optimization tips here.

Saturday, May 01, 2010