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> Cleaning the data - This takes time and it can be annoying.

Have you tried using Google Refine[1]? It's an excellent tool for cleaning datasets and a useful addition to your workflow. I was miffed I didn't know about it when I had to collect and analyze data from surveys awhile ago. I was using Python for cleanup (Google Refine supports Jython).

[1]: http://code.google.com/p/google-refine/

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Google-refine does some really cool stuff, but one of the great developments in the last couple of years within the R community is a big push toward reproducible research and building a powerful toolchain to assist to that end.

The problem with Google-Refine is that it is very hard to recreate precisely the same steps to get from raw to processed data.

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