Source code from Rmd file within another Rmd

Question

I'm attempting to make my code more modular: data loading and cleaning in one script, analysis in another, etc. If I were using R scripts, this would be a simple matter of calling source on data_setup.R inside analysis.R, but I'd like to document the decisions I'm making in an Rmarkdown document for both data setup and analysis. So I'm trying to write some sort of source_rmd function that will allow me to source the code from data_setup.Rmd into analysis.Rmd.

What I've tried so far:

The answer to How to source R Markdown file like `source('myfile.r')`? doesn't work if there are any repeated chunk names (a problem since the chunk named setup has special behavior in Rstudio's notebook handling). How to combine two RMarkdown (.Rmd) files into a single output? wants to combine entire documents, not just the code from one, and also requires unique chunk names. I've tried using knit_expand as recommended in Generate Dynamic R Markdown Blocks, but I have to name chunks with variables in double curly-braces, and I'd really like a way to make this easy for my colaborators to use as well. And using knit_child as recommended in How to nest knit calls to fix duplicate chunk label errors? still gives me duplicate label errors.

Answer 1

After some further searching, I've found a solution. There is a package option in knitr that can be set to change the behavior for handling duplicate chunks, appending a number after their label rather than failing with an error. See https://github.com/yihui/knitr/issues/957.

To set this option, use options(knitr.duplicate.label = 'allow').

For the sake of completeness, the full code for the function I've written is

source_rmd <- function(file, local = FALSE, ...){
  options(knitr.duplicate.label = 'allow')

  tempR <- tempfile(tmpdir = ".", fileext = ".R")
  on.exit(unlink(tempR))
  knitr::purl(file, output=tempR, quiet = TRUE)

  envir <- globalenv()
  source(tempR, local = envir, ...)
}