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Some time ago I created a small template repo (https://github.com/MaximeWack/tidyflow) with a workflow that separates the different steps (importing data, cleaning/tidying data, transforming data, analysing the data, and reporting at the end). The idea was to have "checkpoints" where you save intermediary data so that you don't have to re-run everything every time (e.g if you import data from a live database, between import and cleaning you would have a local copy on which to work without having to run the query every time you wanted to change the cleaning step). At the end of the workflow, all the needed results should be saved, ready to be called from the final Rmd, thus separating computation from presentation.
The bibliography.bib file is your exported bibtex file. The style.csl file is the citation style for the targeted journal (they can all be found here: https://github.com/citation-style-language/styles)