Reproducible research, Rnw, Rmd, makefiles and more

TheEcologist

Global Moderator
#1
Hi Everyone,

I'm starting the thread so we can exchange experience on reproducible research methods in the 21st century. Using tools such as R, knitr, latex, pandoc and others, we can easily create a methodology where the entire writing and analysis of a paper is entirely coded and reproducible.

I've created a template manuscript here on which I will build with knowledge gained, until it's the perfect manuscript skeleton: here

Please share your opinions on what makes the perfect academic manuscript skeleton/template. What should we use, which features to add. Which tool-boxes should we absolutely we using and why?

If many contributors have ideas or add to the skeleton, then I will make this a TS-github project. I'm sure we can make something very useful together. I know trinker has some ideas on what needs to be included in something like this.

Personally I'm writing my papers in .Rnw format, but as many of my co-authors are still using word, I was thinking about writing them in .Rmd. Which is a good compromise as pandoc can convert it quickly to all formats (see my skeleton on github).

I've encountered a few problems though:

1. bibliography citations and references are tricky
2. captions for figures and tables are doable but it's nothing like in latex
3. references to a figure or table are a pain
4. How do you handle double space, a requirement for draft manuscripts

Maybe you guys have already solved these things, maybe you have your own problems. No matter, lets solve them here.

TE
 
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