knit with `pdflatex --shell-escape myfile.tex`?

Question

I want to insert a word count into my .Rnw file.

To do this, I have the following line in myfile.Rnw:

\makeatletter\@@input|"echo `texcount -1 myfile.tex`| cut -c1-4"\makeatother

But this requires me to run pdflatex with the --shell-escape flag. With Sweave, I have a makefile that includes the line:

...
R CMD Sweave myfile.Rnw
pdflatex --shell-escape myfile.tex 
...
...

Is there a way to add the --shell-escape to pdflatex when I use knit instead of the makefile to compile the document?

---

Reproducible example:

contents of myfile.Rnw:

\documentclass{article}
\begin{document}

Words: \makeatletter\@@input|"echo `texcount -1 myfile.tex`| cut -c1-4"\makeatother
Lorem ipsum dolor
\end{document}

what works:

R CMD Sweave myfile.Rnw
pdflatex --shell-escape myfile.tex

what doesn't work:

knit("myfile.Rnw")
"myfile.pdf" %in% dir() ## False

Answer 1

After grepping for pdflatex in the knitr source code, I found the function knit2pdf with the argument compiler. This seems to work:

knit2pdf("myfile.Rnw", compiler = "pdflatex --shell-escape")
"myfile.pdf" %in% dir() ## TRUE

And to do this in Rstudio:

Tools -> options -> Sweave -> enable shell escape commands