Golden Rule of Reproducibility: Script Everything.
Write everything down.
This is analogous to a composer creating a symphony. There are standards in music - clefs, notes, chords, instruments - and they write down how everything is done to replicate.
The main rule in data analysis is to write a script. They are like the musical score for another scientist to replicate your musical analysis.
knitr and Markdown will help you organize your analyses.
Bottom line: Use the R Studio Script Editor. Write it down. Write a script. Make your work reproducible.