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POUsing org-mode to structure an analysis
 

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    <p>I am trying to make better use of org-mode for my projects. I think literate programming is especially applicable to the realm of data analysis and org-mode lets us do some pretty awesome literate programming. </p> <p>I think most of you will agree with me that the workflow for writing an analysis is different than most other types of programming. I don't just write a program, I explore the data. And, while many of these explorations are dead-ends, I don't want to delete/ignore them completely. I just don't want to re-run them every time I execute the org file. I also tend to find or develop chunks of useful code that I would like to put into an analytic template, but some of these chunks won't be relevant for every project and I'd like to know how to make org-mode ignore these chunks when I am executing the entire buffer. Here's a simplified example.</p> <pre><code>* Import - I want org-mode to ignore import-sql. #+srcname: import-data #+begin_src R :exports none :noweb yes &lt;&lt;import-csv&gt;&gt; #+end_src #+srcname: import-csv #+begin_src R :exports none data &lt;- read.csv("foo-clean.csv") #+end_src #+srcname: import-sql #+begin_src R :exports none library(RSQLite) blah blah blah #+end_src * Clean - This is run on foo.csv, producing foo-clean.csv - Fixes the mess of -9 and -13 to NA for my sanity. - This only needs to be run once, and after that, reference. - How can I tell org-mode to skip this? #+srcname: clean-csv #+begin_src sh :exports none sed ..... #+end_src * Explore ** Explore by a factor (1) - Dead end. Did not pan out. Ignore. - Produces a couple of charts showing there is not interaction. #+srcname: explore-by-a-factor-1 #+begin_src R :exports none :noweb yes #+end_src ** Explore by a factor (2) - A useful exploration that I will reference later in a report. - Produces a couple of charts showing the interaction of my variables. #+srcname: explore-by-a-factor-2 #+begin_src R :exports none :noweb yes #+end_src </code></pre> <p>I would like to be able to use org-babel-execute-buffer and have org-mode somehow know to skip over the code blocks import-sql, clean-csv and explore-by-a-factor-1. I want them in the org file, because they are relevant to the project. After-all, tomorrow someone might want to know why I was so sure explore-by-a-factor-1 was not useful. I want to keep that code around, so I can bang out the plot or the analysis or what-ever and go on, but not have it run every-time I rerun everything because there's no reason to run it. Ditto with the clean-csv stuff. I want it around, to document what I did to the data (and why), but I don't want to re-run it every time. I'll just import foo-clean.csv.</p> <p>I Googled all over this and read a bunch of org-mode mailing list archives and I was able to find a couple of ideas, but not what I want. EXPORT_SELECT_TAGS, EXPORT_EXCLUDE_TAGS are great, when exporting the file. And the :tangle header works well, when creating the actual source files. I don't want to do either of these. I just want to execute the buffer. I would like to be able to define code blocks in a similar fashion to be executed or ignored. I guess I would like to find a way to have an org variable such as:</p> <p>EXECUTE_SELECT_TAGS</p> <p>This way I could simply tag my various code blocks and be done with it. It would be even nicer if I could then run the file, using only source blocks with specific tags. I can't find a way to do this and I thought I would ask before asking/begging for a new feature in org-mode.</p>
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    1. COSorry for the weird formatting. I tried putting ">" at the beginning of the org-mode rows, but it's still trying to format the text and it looks weird. If I can figure out how to get SO to drop the formatting, I will update the OP.
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    2. COUse the '1010' button on a highlighted region for code formatting -- which is what I jyst fixed for you.
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      1. USDirk Eddelbuettel
    3. COThanks Dirk. I didn't think of that. I went back in and played a bit more with the formatting. It is much easier to read now.
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