GMT (Generic Mapping Tools) is another nice program that I have used on and off over the years. It's integration with R sent me back to have a second look. I had to install it manually and made several mistakes along the way (such as starting in the Downloads folder instead of moving it to /usr/local first. )
During the install, I found another very nice website which I want to link to here because I might forget it: Ubuntu GIS. Unfortunately, it is not yet supported in Ubuntu 10.10.
I must say that this was not really motivated by research. I was trying to make a map for my summer vacation plans.
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