With Rmarkdown you have 2 options, both have its own merits 1. save code and output separately, so you can save the output (but not comparing the output versio

With Rmarkdown you have 2 options, both have its own merits 1. save code and output separately, so you can save the output (but not comparing the output versions), or always generate output from scratch when needed (this actually help to ensure reproducibility) 2. or you can use R notebook format, which save the result with document together, in some companion folders.