Cross Referenceable Equation with Preview in RMarkdown: http://en.kenjisato.jp/rmarkdown-math/

math_workaround_pdf.Rmd

---
title: Math environment inside $$
author: Kenji Sato
output: 
  bookdown::pdf_document2:
    toc: false
    fig_caption: yes
knit: .render_for_tex
---

# Matheamtical equation with `bookdown::pdf_document2`

You can cross-reference equations in Rmarkdown if you set output to 
`bookdown::pdf_document2` and write equations within
`\begin{align} ~ \end{align}` or `\begin{equation} ~ \end{equation}`


An example:

$$
\begin{equation}
f(x) = f(0) + \int_0^x f'(y) dy,  (\#eq:ftc)
\end{equation}
$$
which we can cross-reference with a syntax different from LaTeX: Equation \@ref(eq:ftc). See [this stackoverflow answer by Yihui Xie](http://stackoverflow.com/a/38884378/1877682) and 
[the related section of his bookdown book](https://bookdown.org/yihui/bookdown/markdown-extensions-by-bookdown.html#equations) for more detail.

`\begin{equation*} ~ \end{equation*}` also produces an equation without
number:

$$
\begin{equation*}
a^n + b^n = c^n 
\end{equation*}
$$


# Drawback

A drawback of using `\begin{align} ~ \end{align}` or the like is that 
RStudio doesn't support math preview for them (yet). You must embrace 
the whole math environment with `$$`. (Figure \@ref(fig:preview))

```{r preview, fig.cap="Math preview", echo=FALSE}
knitr::include_graphics("fig/math.png")
```

The former however causes the "Bad mathe delimiter" error 
in the process of tex compilation.


# Workaround 

### Step 1 {-}

Put the following code snippet in .Rprofile file of the project.

```{r}
.beginMath = c(
  "\\begin{equation}",
  "\\begin{equation*}",
  "\\begin{align}",
  "\\begin{align*}"
)

.endMath = c(
  "\\end{equation}",
  "\\end{equation*}",
  "\\end{align}",
  "\\end{align*}"
)

.render_for_tex = function(input, ...){
  output_file = gsub("\\.[R|r]md$", ".tex", input)
  lines = readLines(input, encoding = "UTF-8");
  
  for (i in seq_along(lines)) {
    # Remove $$ before \begin{equation} or the like.
    if (stringr::str_trim(lines[i]) == "$$") {
      if (any(startsWith(lines[i + 1], .beginMath))) {
        lines[i] = ""
      } else if (any(endsWith(lines[i - 1], .endMath))) {
        lines[i] = ""
      }
    }
  }
  writeLines(lines,"temp.Rmd"); on.exit(unlink('temp.Rmd'))
  rmarkdown::render("temp.Rmd", output_file = output_file)
}
```

### Step 2 {-}

Add `knit: .render_for_math` to the YAML header of your Rmd file. 
Then the Knit button of RStudio is overwritten with the custom renderer 
with preprocessing defined in .Rprofile.

Rprofile

.beginMath = c(
  "\\begin{equation}",
  "\\begin{equation*}",
  "\\begin{align}",
  "\\begin{align*}"
)

.endMath = c(
  "\\end{equation}",
  "\\end{equation*}",
  "\\end{align}",
  "\\end{align*}"
)

.render_for_tex = function(input, ...){
  output_file = gsub("\\.[R|r]md$", ".tex", input)
  lines = readLines(input, encoding = "UTF-8");
  
  for (i in seq_along(lines)) {
    # Remove $$ before \begin{equation} or the like.
    if (stringr::str_trim(lines[i]) == "$$") {
      if (any(startsWith(lines[i + 1], .beginMath))) {
        lines[i] = ""
      } else if (any(endsWith(lines[i - 1], .endMath))) {
        lines[i] = ""
      }
    }
  }
  writeLines(lines,"temp.Rmd"); on.exit(unlink('temp.Rmd'))
  rmarkdown::render("temp.Rmd", output_file = output_file)
}