lucacerone lucacerone - 4 months ago 44
R Question

knitr: run all chunks in an Rmarkdown document

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?


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")
purl("SO-tag-package-dependencies.Rmd", output=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")
  knitr::purl(rmd, output=tempR)
  sys.source(tempR, envir=envir)