At this point I’ve written a hundred times about the supplement for Goring et al., (2013), but just in case you haven’t heard it:
Goring et al., (2013) uses a large vegetation dataset to test whether or not pollen richness is related to plant richness at a regional scale. Because of the nature of the data and analysis, and because I do all of my work (or most of it) using R, I thought it would be a good idea to produce totally reproducible research. To achieve this I included a version of the paper, written using RMarkdown, as a supplement to the paper. In addition to this, I posted the supplement to GitHub so that people who were interested in looking at the code more deeply could create their own versions of the data and could use the strengths of the GitHub platform to help them write their own code, or do similar analyses.
This is a basic how-to to get you started writing your paper using RMarkdown, RStudio and GitHub (EDIT: if some of these instructions don’t work let me know and I’ll fix them immediately):