Writing a Reproducible Paper in R Markdown

The present paper provides a template for a reproducible scientific paper written in R Markdown. Below I outline some of the "tricks"/code (e.g., referencing tables, sections etc.) I had to figure out to produce this document. The underlying files which produce this document can be downloaded here (see paper). I think I got pretty far but there is always room for improvement and more automatization, in parallel to the incredible developments in R and Rstudio (bookdown etc.). I intend to update this file when I discover more convenient code.