knitr: run all chunks in an Rmarkdown document

knitr, r, r-markdown, rstudio

Solution

Using `Run all chunks` is equivalent to:

- Create a temporary R file

- Use `knitr::purl` to extract all the R chunks into the temp file

- Use `source()` to run the file

- Delete the temp file

Like this:

tempR <- tempfile(fileext = ".R")
library(knitr)
purl("SO-tag-package-dependencies.Rmd", output=tempR)
source(tempR)
unlink(tempR)

But you will want to turn this into a function. This is easy enough, except you have to use `sys.source` to run the R script in the global environment:

runAllChunks <- function(rmd, envir=globalenv()){
  tempR <- tempfile(tmpdir = ".", fileext = ".R")
  on.exit(unlink(tempR))
  knitr::purl(rmd, output=tempR)
  sys.source(tempR, envir=envir)
}

runAllChunks("SO-tag-package-dependencies.Rmd")

Problem

I have an .Rmd document which knitr process just fine. I would like to run all the chunks in the document, so that I can explore the results in my R shell. In Rstudio there is an option to run all the chunks in the document, but I can't find a way to achieve the same effect in a simple R session (opened in my terminal). Is there a way to do this?

Original source