Welcome to the RStudio community !
As for your question: Do you expect that a single call to arules::apriori() would run in parallel (spanning across multiple cores) or do you want to run individual executions of arules::apriori() in parallel ?
If it is the first case, then this sounds like a feature request you can raise at GitHub with the package maintainer.
If it is the latter, there is various tools out there that could do that: Packages that come to mind are doMC to register a multicore parallel backend where you can run parallel foreach loops or any of the mc*apply functions. Alternatively you could use furrr as as parallel pendant to purrr for more functional programming.
Any of the above is independent of your use of RMarkdown but RMarkdown does not hinder it either.