
Using knitr and pandoc to create reproducible scientific reports - leephillips
http://galahad.well.ox.ac.uk/repro/
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z0r
I've been learning to use org-babel to accomplish similar things recently -
[http://orgmode.org/worg/org-contrib/babel/languages/ob-
doc-g...](http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-
gnuplot.html)

My workflow is crude, but org-babel lets me capture the process of selecting
elements from a raw dump of json to csv with a block of shell script (invoking
jq), post-processing the output with a block of python and then passing the
results into blocks of gnuplot to generate graphs. I believe org-babel has
support for R among many other languages, so you can include snippets of
nearly anything in your report generating pipeline. It is pretty nifty!

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davecap1
Is there something like this for Python, other than iPython notebooks?

edit: just found a couple if anyone is interested
([https://github.com/AndreasHeger/CGATReport](https://github.com/AndreasHeger/CGATReport),
[http://mpastell.com/pweave/](http://mpastell.com/pweave/),
[https://github.com/stdbrouw/python-
literate](https://github.com/stdbrouw/python-literate))

~~~
tincholio
You can use org-babel with Python as well.

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jgalt212
This is great stuff. Obviously, reproducible research is one of the keys, if
not the linchpin, to scientific advancement.

Where I think knitr/pandoc really fills a void is increasing the chances a
citizen scientist can have real impact. If some Joe Schmo off the street
publishes original research, it's likely to be dismissed by the establishment.
However, if Joe's research is easily testable, his/her proposed advancements
are more likely to be entered into the world's body of knowledge.

In the end all of us will benefit, and at a faster rate.

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Mikeb85
Knitr is super cool, I've used it for a few small projects now. Also love how
R-Studio integrates it. R Studio, along with the greater R ecosystem, is by
far the nicest programming environment I've ever used (although it is somewhat
specialized - excels mainly in dealing with data as opposed to creating apps).

