How can knitr's cached results be used to reproduce the environment in a given chunk?

knitr, r

Solution

Here is one solution, which is still a little bit awkward but it works. The idea is to add a chunk option named `mute` which takes `NULL` by default, but it can also take an R expression, e.g. `mute_later()` below. When `knitr` evaluates the chunk options, `mute_later()` can be evaluated and `NULL` is returned; at the same time, there are side effects in `opts_chunk` (setting the global chunk options like `eval = FALSE`).

Now what you need to do is to put `mute=mute_later()` in the chunk after which you want to skip the rest of the chunks, e.g. you can move this option from `example-a` to `example-b`. Because `mute_later()` returns `NULL` which happens to be the default value of the `mute` options, the cache will not be broken even you move this option around.

\documentclass{article}
\begin{document}

<<setup, include=FALSE, cache=FALSE>>=
rm(list = ls(all.names = TRUE), envir = globalenv())
opts_chunk$set(cache = TRUE) # enable cache to make it faster
opts_chunk$set(eval = TRUE, echo = TRUE, include = TRUE)

# set global options to mute later chunks
mute_later = function() {
  opts_chunk$set(cache = FALSE, eval = FALSE, echo = FALSE, include = FALSE)
  NULL
}
# a global option mute=NULL so that using mute_later() will not break cache
opts_chunk$set(mute = NULL)
@

<<example-a, mute=mute_later()>>=
x = rnorm(4)
Sys.sleep(5)
@

<<example-b>>=
y = rpois(10,5)
Sys.sleep(5)
@

<<example-c>>=
z = 1:10
Sys.sleep(3)
@

\end{document}

It is awkward in the sense that you have to cut-and-paste `, mute=mute_later()` around. Ideally you should just set the chunk label like the gist I wrote for Barry.

The reason that my original gist did not work is because chunk hooks are ignored when a chunk is cached. The second time you `knit()` the file, the chunk hook `checkpoint` for `example-a` was skipped, therefore `eval=TRUE` for the rest of chunks, and you saw all chunks were evaluated. By comparison, chunk options are always dynamically evaluated.

Problem

Original source