if you still need a great example of a fully REPRODUCIBLE analysis plus a PAPER, use [this repo][1]. 

The @jscamac did a great job by making his analysis rproducible and I personally validated it. 

You can lean how to use R specific functions like the package `remake` to ensure reproduciblity. 

Watch out / the calculations take about one hour to complete. 

Its all scripted and produces a LaTeX paper in the end with figures. 


  [1]: https://github.com/jscamac/Alpine_Shrub_Experiment