There has been a lot of progress on the R Markdown development since the first edition of this book. To make it clear, there are two versions of R Markdown: we call the implementation in the markdown package (Allaire et al., 2015b) “R Markdown v1” (https://github.com/rstudio/markdown), and we call the implementation rmarkdown (Allaire et al., 2015a) “R Markdown v2” (http://rmarkdown.rstudio.com). Unless otherwise noted, use of the term “R Markdown” in this chapter refers to R Markdown v2.
R Markdown v1 is based on the C library sundown, and the major focus is HTML output. Its functionality is very limited, e.g., there is no support for citations or footnotes. R Markdown v2 is based on Pandoc, which has boosted Markdown to a whole ...
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