Clearing all but certain objects

If you run into a situation where you’re using a ton of memory (e.g. manipulating transcriptomic data, resampling, or working with electrophysiology traces) use rm() to selectively get rid off objects in the environment. A useful pattern is to write out large objects you’ll need in the future, remove them, and then read them back in when you need them. This is usually not important, but when it is, it is.

If you’re working interactively and tempted to use rm(list = ls()) consider restarting your r session (ctrl+shift+F10 on windows). Overreliance on rm(list = ls()) is poor form.

A side note – unlike listing items where the function matching the unix command acts on the environment and a new command acts on the files system (ls() and list.files()) the functions for removing items don’t follow this logic. rm() acts on objects in your environment whereas unlink() acts on system files.

Similarly if you want to retain only specific objects you can take this approach:

 # get rid of everything
rm(list=ls())

# get rid of everything except specific objects and all loaded functions
rm(list = 
   ls()[!(ls() %in% c(
   # objects
   c("data1", "data2", "bool1", "list1"), 
   # functions
   lsf.str())
   ) ])