Typically, you can set GITHUB_PAT variable in your .Renviron file using the following format:
GITHUB_PAT=8c70fd8419398999c9ac5bacf3192882193cadf2
You can also set it in your .Rprofile file using the following format:
Sys.setenv(GITHUB_PAT="8c70fd8419398999c9ac5bacf3192882193cadf2")
For more on what to do with the PAT, see gh::gh_whoami.