Question

What commands are run when pressing “Knit HTML” on an R Markdown file in Rstudio 0.96?

My motivation is that I might want to run the same command when I’m in another text editing environment or I might want to combine the command in a larger makefile.

Answer 1

Put Sys.sleep(30) in a chunk and you will see clearly what commands are called by RStudio. Basically they are

1. library(knitr); knit() to get the markdown file;
2. RStudio has internal functions to convert markdown to HTML;

The second step will be more transparent in the next version of the markdown package. Currently you can use knitr::knit2html('your_file.Rmd') to get a similar HTML file as RStudio gives you.

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Update on 2019/09/17: The above answer applies to RStudio v0.96 (in the year 2012). Now R Markdown is compiled through rmarkdown::render(), which uses Pandoc instead of the retired R package markdown. See the post Relationship between R Markdown, Knitr, Pandoc, and Bookdown for more details.