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    • CommentAuthorderele
    • CommentTimeNov 20th 2009
     
    Hi,
    I started using R/sweave for writeup of bioinformatics (high throughput sequencing) a few weeks ago. I am planning to write large parts of my PhD-thesis in this system as it improves both my code and housekeeping.

    I am using cached code chunks (with the R weaver package). Inside these code chunks I often use the R-function "pipe" to run programs or perl-scripts on data that I want to pre-process befor getting it into R.
    Do you know of mechanisms to do some kind of testing for changes in "helper-scripts" or even the raw data? Some kind of checksum mechanism?

    I very recently started to use git (the first VCS I am using) and like it very much. I think it is great in combination with the R/sweave system as it allows you to roll back changes in the Rnw tex and pdf files simultaniousely and to avoid Re-compilation at that timepoint. My first project in the system was a presentation about the system. I included some large, non-trivial data and I still have it on github waiting for someone trying to reproduce it. If you want to do so you can use the public clone url:
    git://github.com/derele/Talk--Emacs-environment-for-PhD-thesis.git
    or go to
    http://github.com/derele/Talk--Emacs-environment-for-PhD-thesis/tree/non-emacs-focussed
    to look at the pdf, code or download it.
    I would be very grateful for feedback.

    Emanuel
    • CommentAuthorcanno
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    • CommentTimeApr 25th 2013
     
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    • CommentAuthorcsluyuan
    • CommentTimeMay 7th 2013
     
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