Documenting equations with deqn and roxygen

This answer doesn't address your ASCII issue, but it currently is my go-to way when rendering latex equations in HTML, so I hope this helps you.

Take a look at the mathjaxr package (CRAN, GitHub). You can install it either with install.packages("mathjaxr") or remotes::install_github("wviechtb/mathjaxr").

It introduces a macro \loadmathjax that loads the necessary JavaScript from MathJax to render latex equations. Then use the macro \mjeqn{latex}{ascii} or \mjdeqn{latex}{ascii} instead of \eqn or \deqn and you're good to go.

In your specific example, we'd have the following:

#' Example
#'
#' Example mathjax function
#'
#' \loadmathjax
#' \mjdeqn{ \sigma = \sqrt{ \frac{Z}{n} \sum
#'   \textstyle\frac{1}{2}\displaystyle
#'     \left\[ \left( \log \frac{H_i}{L_i} \right)^2  - (2\log 2-1) \left( \log \frac{C_i}{O_i} \right)^2 \right] }
#' }{ASCII representation}
example <- function(a, b, c) {}

(notice the open square bracket is escaped)

If you use RStudio, you may run into some trouble with the \loadmathjax macro. To preview the content quickly, do the following:

1. Generate documentation (Ctrl + Shift + D or devtools::document(roclets = c('rd', 'collate', 'namespace')))
2. Call preview_rd("example.Rd") to preview the documentation

When you're done, you can inspect the final result with these steps:

1. Generate documentation (Ctrl + Shift + D or devtools::document(roclets = c('rd', 'collate', 'namespace'))
2. Install the package (Ctrl + Shift + L or devtools::install())
3. Restart the R session with .rs.restartR()
4. Preview documentation with ?example

Either way should produce the following result:

According to Hadley Wickham, line wrapping will be removed in future versions of roxygen. So the solution for roxygen2 is to roxygenize the file (or package), then manually update the text equation in the affected .Rd file(s).