An R Markdown document (
*.Rmd) is first compiled to Markdown (
*.md) through the knitr package, and then Markdown is compiled to other output formats (such as LaTeX or HTML) through Pandoc. This process is automated by the rmarkdown package. You do not need to install knitr or rmarkdown separately, because they are the required packages of bookdown and will be automatically installed when you install bookdown. However, Pandoc is not an R package, so it will not be automatically installed when you install bookdown. You can follow the installation instructions on the Pandoc homepage (http://pandoc.org) to install Pandoc, but if you use the RStudio IDE, you do not really need to install Pandoc separately, because RStudio includes a copy of Pandoc. The Pandoc version number can be obtained via:
rmarkdown::pandoc_version() ##  '2.1.3'
If you find this version too low and there are Pandoc features only in a later version, you can install the later version of Pandoc, and rmarkdown will call the newer version instead of its built-in version.