Rmarkdown numbered equation helper

convert_align.R

#I write papers and reports using Rmarkdown, knitting to pdf.
#My co-authors use word, so I usually knit a version to docx for them to edit.
#This mostly works flawlessly, except when I use \begin{align} and \end{align} to delimit display equations.
#Using \begin{align} and \end{align} results in nicely centered and numbered equations in pdf, BUT
#the equations don't render at all when I try to make a docx.

#As a quick hack so I can make a passable docx to share with my co-authors, the following script replaces all instances
#of \begin{align} and \end{align} with "$$". The modified version of the original Rmarkdown file knits to docx just fine,
# albeit without equation numbers.

convert_align<-function(infile, outfile){
       x <- readLines(infile)
       x[grep("align}", x)]<-"$$"
       cat(x, file=outfile, sep="\n") }

#make a version that will render as docx
convert_align("temp.Rmd", "temp_for_word.Rmd")

#render the pdf
rmarkdown::render("temp.Rmd", "pdf_document")

#render the docx
rmarkdown::render("temp_for_word.Rmd", "word_document")