Language engines

Use other languages in knitr


We can use any languages in knitr, including but not limited to R. Here are some simple demos with Python, Awk, Ruby, Haskell, Bash, Perl, Graphviz, TikZ, SAS, Scala, and CoffeeScript, etc:

These languages are easy to deal with because they can be called by pure command line, e.g. python -c can execute the code passed in as a character string.

The Rcpp engine is different, however. The C++ code is compiled through the Rcpp package. See Rcpp.Rmd (output) for example. Similarly, C code is compiled via R CMD SHLIB (example/output).

A special engine cat can be used to save the content of a code chunk to a file using the cat() function; see the example 095 for an application.

The object knit_engines stores a series of named functions to handle code from different languages, and you are free to define a function to deal with a custom language. See engine.R for examples on how I deal with Python and Awk.

I do not really know much about other languages, so please feel free to contribute more language engines to knitr.

Note these languages work not only in Markdown, but also in other formats like LaTeX.

Except engine='R' (default), all chunks are executed in separate sessions, so the variables cannot be directly shared. If we want to make use of objects created in previous chunks, we usually have to write them to files (as side effects). For the bash engine, we can use Sys.setenv() to export variables from R to bash (example). For the sql and the stan engines, we can store the object as a variable whose name is specified to the output.var chunk option. Another approach is to use the (experimental) runr package.

Additional arguments can be passed to the engines via the engine.opts chunk option. The option can be specified as a string (e.g., '-p') or as a list of strings named by engines (e.g., list(perl = '-Mstrict -Mwarnings', bash = '-o errexit')). The latter is useful to template arguments via knitr::opts_chunk$set(). For the cat engine, the code chunk can be displayed in the output if the chunk language is specified via the engine.opts chunk option, e.g. engine.opts = list(lang = 'makefile'). For the tikz engine, the path to the convert utility of ImageMagick can be specified via the engine.opts chunk option, e.g. engine.opts = list(convert = 'path/to/convert'). Similarly, more command line arguments to convert can be specified via, for example, engine.opts = list(convert.opts = '-density 300').