Two Hidden Ways to Set Global Chunk Options for knitr

Yihui Xie 2023-10-09

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:

  1. 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.

  2. 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.