How can I tell which packages I am not using in my R script?

Have you considered using packrat?

packrat::clean() would remove unused packages, for example.

Update 2020-04-13

I've now updated the referenced function to use the abstract syntax tree (AST) instead of using regular expressions as before. This is a much more robust way of approaching the problem (it's still not completely ironclad). This is available from version 0.2.0 of funchir, now on CRAN.

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I've just got around to writing a quick-and-dirty function to handle this which I call stale_package_check, and I've added it to my package (funchir).

e.g., if we save the following script as test.R:

library(data.table)
library(iotools)
DT = data.table(a = 1:3)

Then (from the directory with that script) run funchir::stale_package_check('test.R'), we'll get:

Functions matched from package data.table: data.table

**No exported functions matched from iotools**