Two Hidden Ways to Set Global Chunk Options for knitr

Sometimes you may not like the default values of knitr’s chunk options, and you know how to change them (i.e., knitr::opts_chunk$set()), but it can be tedious to do it for every single document. How can we change default chunk options globally in a system?

One approach is to set these options in your .Rprofile, if you know what this file is and how to edit it. However, this approach has a drawback—it will load knitr for any R session, even if you do not need to use knitr in a certain session. To avoid that, you could set a package hook for knitr in .Rprofile, e.g.,

setHook(packageEvent('knitr', 'onLoad'), function(...) {
  knitr::opts_chunk$set(message = FALSE, warning = FALSE)
})

With this hook, knitr will not be loaded immediately when R starts up. The change of chunk options will occur only when knitr is being loaded (e.g., when you compile a document).

If you find the above approach too technical to understand, there are two other ways to modify chunk options globally:

You can set global R options of the form options(knitr.chunk.NAME = VALUE) in .Rprofile, where NAME is the chunk option name, and VALUE is the desired value. For example,
```
options(knitr.chunk.message = FALSE, knitr.chunk.warning = FALSE)
```
These options will be recognized by knitr, which will run opts_chunk$set() for you internally.
Another way is for people who prefer environment variables over .Rprofile. You can set the environment variable R_KNITR_OPTIONS to a comma-separated value like this:
```
R_KNITR_OPTIONS="knitr.chunk.message=FALSE,knitr.chunk.warning=FALSE"
```
Basically this value will be passed to options() and go to the previous way.

These two methods have existed for years but never been documented, because I was not sure if they could be useful to anyone else (I use them occasionally). Recently I seem to have seen a use case, so I’m writing them down here.

Yihui Xie 2023-10-09