1.4 Two rendering approaches

Merging all chapters into one Rmd file and knitting it is one way to render the book in bookdown. There is actually another way: you may knit each chapter in a separate R session, and bookdown will merge the Markdown output of all chapters to render the book. We call these two approaches “Merge and Knit” (M-K) and “Knit and Merge” (K-M), respectively. The differences between them may seem subtle, but can be fairly important depending on your use cases.

  • The most significant difference is that M-K runs all code chunks in all chapters in the same R session, whereas K-M uses separate R sessions for individual chapters. For M-K, the state of the R session from previous chapters is carried over to later chapters (e.g., objects created in previous chapters are available to later chapters, unless you deliberately deleted them); for K-M, all chapters are isolated from each other.2 If you want each chapter to compile from a clean state, use the K-M approach. It can be very tricky and difficult to restore a running R session to a completely clean state if you use the M-K approach. For example, even you detach/unload packages loaded in a previous chapter, R will not clean up the S3 methods registered by these packages.
  • Because knitr does not allow duplicate chunk labels in a source document, you need to make sure there are no duplicate labels in your book chapters when you use the M-K approach, otherwise knitr will signal an error when knitting the merged Rmd file. Note that this means there must not be duplicate labels throughout the whole book. The K-M approach only requires no duplicate labels within any single Rmd file.
  • K-M does not allow Rmd files to be in subdirectories, but M-K does.

The default approach in bookdown is M-K. To switch to K-M, you either use the argument new_session = TRUE when calling render_book(), or set new_session: yes in the configuration file _bookdown.yml.

You can configure the book_filename option in _bookdown.yml for the K-M approach, but it should be a Markdown filename, e.g., _main.md, although the filename extension does not really matter, and you can even leave out the extension, e.g., just set book_filename: _main. All other configurations work for both M-K and K-M.

  1. Of course, no one can stop you from writing out some files in one chapter, and reading them in another chapter. It is hard to isolate these kinds of side-effects.