From the Political Science Replication blog:

When reproducing pubished work, I’m often annoyed that methods and models are not described in detail. Even if it’s my own project, I sometimes struggle to reconstruct everything after I took a longer break from a project. An article by post-docs Rich FitzJohn and Daniel Falster shows how to set up a project structure that makes your work reproducible.

To get that “mix” into a reproducible format, post-docs Rich FitzJohn and Daniel Falster from Macquarie University in Australia suggest to use the same template for all projects. Their goal is to ensure integrity of their data, portability of the project, and to make it easier to reproduce your own work later. This can work in R, but in any other software as well.

Here's their gist. My post from late last year suggests a similar structure. PSR and I were both informed about ProjectTemplate based on these posts--check it out here.