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.