Rmd files are rendered via Rmarkdown::render  in a shell script: 

Rscript -e "rmarkdown::render(input = 'my-awesome-notebook.rmd', output_dir = '../results', clean = TRUE)"

You may also need to install pandoc  via apt-get, as well as LaTeX if you're rendering to PDF (here's how). Either is straightforward when using Code Ocean's custom package management system.

You can also press the 'Knit' button from within an interactive Rstudio session on Code Ocean.

 Example capsules:

https://codeocean.com/2018/08/01/mapping-the-universe-of-registered-reports

https://codeocean.com/2018/06/21/data-availability-reusability-and-analytic-reproducibility-colon-evaluating-the-impact-of-a-mandatory-open-data-policy-at-the-journal-cognition

https://codeocean.com/2018/10/16/the-contact-hypothesis-re-evaluated-colon-code-and-data

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