AsciiDoc is similar to Markdown: a simple, readable text markup that can be converted to html.

For simple reports, I’m satisfied with R Markdown, but for a long report with a lot of sections, it’s nice to have a sidebar with a floating table of contents. (See this example and its AsciiDoc source.)

An important part of the appeal of Markdown is the limited set of simple marks. But sometimes you want just a little bit extra, like subscripts (e.g., in describing an F1 hybrid). You can insert a bit of html code, but it’s even better to use a similar system with a more rich syntax, like AsciiDoc.

The syntax for AsciiDoc is similar in style to that of Markdown, but a bit different; I’m always getting confused between the two, and look at my example and the AsciiDoc cheatsheet.

Code chunk delimiters

KnitR-wise, the main difference when you use asciidoc is that the code chunks are delimited differently. Here’s an example:

We see that this is an intercross with +r nind(sug)+ individuals.
There are +r nphe(sug)+ phenotypes, and genotype data at
+r totmar(sug)+ markers across the +r nchr(sug)+ autosomes.  The genotype
data is quite complete.

Use +plot()+ to get a summary plot of the data.

//begin.rcode summary_plot, fig.height=8
plot(sug)
//end.rcode

The larger code chunks are delimited with //begin.rcode and //end.rcode.

The in-line code chunks are indicated with +r and +, as AsciiDoc uses + to mark code, to be shown in a monospace font.

Otherwise, everything about the code chunks and chunk options is the same as with R Markdown.

Floating table of contents and other stuff

The top of my AsciiDoc example is the following:

An example Knitr/Asciidoc document
==================================
link:http://kbroman.org[Karl W Broman]
:toc2:
:numbered:
:data-uri:

:toc2: indicates to include a table of contents, floating in the left margin. :numbered: indicates to number the sections. :data-uri: indicates to embed the images within the html file.

Tables

You can’t use kable or xtable with AsciiDoc. Instead, use the ascii function in the ascii package, which has a shocking number of arguments.

Here’s a simple example:

//begin.rcode table, results="asis", warning=FALSE
x <- rnorm(100, 10, 5)
y <- 2*x + rnorm(100, 0, 2)
out <- lm(y ~ x)
coef_tab <- summary(out)$coef
library(ascii)
ascii(coef_tab, include.rownames=TRUE, include.colnames=TRUE,
      header=TRUE)
//end.rcode

Note the use of results="asis". I used warning=FALSE to suppress a warning message.

Here’s what that chunk would produce, plus an AsciiDoc file with just that chunk.

Installing AsciiDoc

To use AsciiDoc, you’ll need to install AsciiDoc; see this installation page.

On Mac OSX, I recommend using Homebrew; then you just type brew install asciidoc.

A key point: you’ll need Python 2 and not Python 3. On my computer, python is Python 3; I have to switch to Python 2 before running AsciiDoc. If I forget to switch, I get the following error message:

File "/usr/local/bin/asciidoc", line 101
  except KeyError, k: raise AttributeError, k
                 ^
SyntaxError: invalid syntax

I’d also recommend installing the ascii package for R.

Converting AsciiDoc to html

RStudio has no facilities for AsciiDoc; you’ll need to use command-line tools.

You first use knit in the knitr package to process the asciidoc/KnitR document:

R -e 'library(knitr);knit("knitr_example.Rasciidoc", "knitr_example.asciidoc")'

You then use asciidoc to convert this to an html file:

asciidoc knitr_example.asciidoc