How to convert R Markdown to HTML? I.e., What does "Knit HTML" do in Rstudio 0.96?

Basic Script

So now that the R markdown package has been released, here is some code to replicate the features of Knit to Html.

require(knitr) # required for knitting from rmd to md
require(markdown) # required for md to html 
knit('test.rmd', 'test.md') # creates md file
markdownToHTML('test.md', 'test.html') # creates html file
browseURL(paste('file://', file.path(getwd(),'test.html'), sep='')) # open file in browser 

where test.rmd is the name of your R markdown file. Note that I'm not 100% confident about the browseURL line (hence my question here about opening files in a web browser).

markdownToHTML Options

The good thing about markdownToHTML is that there are heaps of options in how the HTML is created (see ?markdownHTMLOptions). So for example, if you want just a code fragment without all the header information, you could write:

markdownToHTML('test.md', 'test.html', options='fragment_only')

or if you don't like hard wrapping (i.e., inserting line breaks when there are single manual line breaks in the markdown source), you can omit the 'hard_wrap' option.

# The default options are 'hard_wrap', 'use_xhtml', 
#      'smartypants', and 'base64_images'.
markdownToHTML('test.md', 'test.html', 
       options=c('use_xhtml', 'base64_images'))

Makefile

This could also all be added to a makefile perhaps using Rscript -e (e.g., something like this). Here's a basic example makefile I put together, where test indicates that the rmd file is called test.rmd.

RMDFILE=test

html :
    Rscript -e "require(knitr); require(markdown); knit('$(RMDFILE).rmd', '$(RMDFILE).md'); markdownToHTML('$(RMDFILE).md', '$(RMDFILE).html', options=c('use_xhtml', 'base64_images')); browseURL(paste('file://', file.path(getwd(),'$(RMDFILE).html'), sep=''))"

The makefile uses my preferred markdown options: i.e., options=c('use_xhtml', 'base64_images')

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.

Very easy command line method from knitr in a knutshell:

R -e "rmarkdown::render('knitr_example.Rmd')"

This requires rmarkdown to be installed with install.packages(rmarkdown) and that pandoc is installed (apparently it comes with Rstudio, see knitr in a knutshell for more details).

So far when I've used this it nicely puts all the plots in the HTML file rather than as images in a figure directory and cleans up any intermediate files, if any; just like compilation in RStudio does.