Stanhl — Stan Syntax Highlighting in knitr

A screenshot of stanhl syntax highlighting in a LaTeX document

I needed a simple hack to highlight Stan syntax in knitr files for a course I'm takingstanhl is that hack. It's quick and dirty (e.g. this took me thirty minutes to write), but I thought I'd share before polishing it.


You need installed. The following should work:

$ pygmentize -V
Pygments version 1.6, (c) 2006-2013 by Georg Brandl.

If you don't have Pygments installed, just install with the Python Package Index:

$ pip install Pygments


Using the terrific devtools package, you can install stanhl with:


If you don't have devtools installed, use install.packages('devtools') first.

Using stanhl in LaTeX (Rnw) files

There are two steps:

  1. Include the following in your LaTeX header:

  2. Write your Stan model, store it to a variable (e.g. to call with stan(model_code=x, ...), and then use:

    m <- "
    data {
      // stan stuff
    model {
      // more stan stuff

Then, in another block call stan(), do other stuff, etc.

Using stanhl in RMarkdown files

A screenshot of stanhl syntax highlighting in an HTML document

I haven't extensively tested Markdown support (swamped for the next few weeks), but stanhl_html() should work as a replacement for stanhl_latex(). If it doesn't, feel free to submit a pull request. Below is the basic idea.

The header:


The meat and potatoes (or tofu and eggplant):

m <- "
data {
  int<lower=0> N;
  vector[N] weight;
  vector[N] diam1;
  vector[N] diam2;
  vector[N] canopy_height;
transformed data {
  vector[N] log_weight;
  vector[N] log_canopy_volume;
  log_weight        <- log(weight);
  log_canopy_volume <- log(diam1 .* diam2 .* canopy_height);
parameters {
  vector[2] beta;
  real<lower=0> sigma;
model {
  log_weight ~ normal(beta[1] + beta[2] * log_canopy_volume, sigma);


Highlighting Stan Models from File

You can also highlight a model directly from a .stan file:

mesquite_file <- system.file("inst", "extdata", "mesquite_volume.stan",

# Then run your Stan model directly from file with something like:
# fit <- stan(mesquite_file, data=mesquite_data)


You can change Pygments style used in syntax highlighting with:

 > stanhl_styles() # get available style list (depends on Pygments plugins)
 [1] "monokai"  "manni"    "rrt"      "perldoc"  "borland"  "colorful"
 [7] "default"  "murphy"   "vs"       "trac"     "tango"    "fruity"
[13] "autumn"   "bw"       "emacs"    "vim"      "pastie"   "friendly"
[19] "native"
> stanhl_opts$set(style="emacs")

See the vignette for these styles rendered.


I interfaced Pygments with R to create syntax highlighting for Stan, but afterwards thought it might be useful to have a more general R-Pygments interface. This interface is now the pygmentr package; I am debating whether to merge these two together, or just keep stanhl separate. For now, there are some Stan-specific features I want, e.g. including Stan models from file, so this package is worth it.

vsbuffalo/stanhl documentation built on May 3, 2019, 7:08 p.m.