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

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.