Command-line program to update R Markdown code to use `$latex` delimter

Question

UPDATE (13th June 2012): RStudio now supports a range of mathjax delimtiers including single dollar signs and double dollar signs without latex.

---

In 0.96 RStudio changed its Mathjax syntax from $<equation>$ to $latex <equation>$ for inline equations and from $$<equation>$$ to $$latex <equation>$$ for displayed equations.

Thus, in summary:

The revised syntax adds a latex qualifier to the $ or $$ equation begin delimiter.

I have some existing scripts that use the original $ delimiter and I would like to update them to use the new $latex delimiter. I was thinking that sed or awk might be suitable.

Also dollars that appear in r code blocks like this should not be altered.

```{r ...}
x <- Data$asdf
```

Question

• What would be a good simple command-line program perhaps using sed or awk to update my R Markdown code to use the newer mathjax delimiter in R Studio?

Working example 1

Original text:

$y = a + b x$ is the formula.
This is some text, and here is a displayed formula
$$y = a+ bx\\
x = 23$$

```{r random_block}
y <- Data$asdf
```

and some more text     
$$y = a+ bx\\
x = 23$$

after transformation becomes

$latex y = a + b x$ is the formula.
This is some text, and here is a displayed formula
$$latex y = a+ bx\\
x = 23$$

```{r random_block}
y <- Data$asdf
```

and some more text     
$$latex y = a+ bx\\
x = 23$$

Working example 2

`r opts_chunk$set(cache=TRUE)`
<!-- some comment -->

Some text

<!-- more -->
Observed data are $y_i$ where $i=1, \ldots, I$.  
$$y_i \sim N(\mu, \sigma^2)$$

Some text $\sigma^2$ blah blah $\tau$. 

$$\tau = \frac{1}{\sigma^2}$$

blah blah $\mu$ and $\tau$

$$\mu \sim N(0, 0.001)$$
$$\tau \sim \Gamma(0.001, 0.001)$$

should become

`r opts_chunk$set(cache=TRUE)`
<!-- some comment -->

Some text

<!-- more -->
Observed data are $latex y_i$ where $latex i=1, \ldots, I$.  
$$latex y_i \sim N(\mu, \sigma^2)$$

Some text $latex \sigma^2$ blah blah $latex \tau$. 

$$latex \tau = \frac{1}{\sigma^2}$$

blah blah $latex \mu$ and $latex \tau$

$$latex \mu \sim N(0, 0.001)$$
$$latex \tau \sim \Gamma(0.001, 0.001)$$

Answer 1

Using perl and a look-back, should do the trick:

perl -pe 's/\b(?<=\$)(\w+)\b /latex $1 /g' file.txt

Make the changes in-line with the -i flag:

perl -pe -i 's/\b(?<=\$)(\w+)\b /latex $1 /g' file.txt

EDIT:

Try this monster:

perl -pe 's/\b(?<=\$)(\w+)\b(\$?)([ =])/latex $1$2$3/g;' -pe 's/(?<=\$)(\\\w+)/latex $1/g' file.txt

HTH

Answer 2

This might work for you:

sed '/^```{r/,/^```$/b;/^`r/b;:a;/\\\\$/{$!{N;ba}};s/\(\$\$\)\([^$]*\(\$[^$]*\)*\$\$\)\|\(\$\)\([^$]*\$\)/\1\4latex \2\5/g' file

N.B. The r codeblock code may need to be extended/altered as from the example code it is not obvious what it constitutes.