This is a minimal bookdown example. Although you see a few files here, only index.Rmd is required. All other files are optional, but bookdown-minimal.Rproj can make it much easier to build the book.
The key is the site setting in index.Rmd. If you want to build the book in RStudio, just click the Build Book button in the Build pane, otherwise call the function in R:
bookdown::render_book('index.Rmd', 'all')