Appendix B

R start-up

The R start-up protocol will include running files with the names .Rprofile, .Renviron, and files with the extensions .Rhistory and .Rdata, in the user home directory (R_USER), R_HOME/etc, and the current working directory (Sections 2.7.1, 2.8.1, and 2.8.2).

One can bypass start-ups that would otherwise use Rprofile.site, .Renviron (and/or Renviron.site). and .Rprofile files, by invoking R from a system shell (i.e., Fig 2.3), using the commands R --no-environ, --no-site-file, and --no-init-file, respectively (use R.exe instead of R from PowerShell). The --vanilla flag combines the --no-environ, --no-site-file, and --no-init-file flags, along with several other start-up simplifications to allow a “factory fresh” start. Help for these and other advanced options can obtained using R -h (R.exe -h from PowerShell).

The entire R start-up process, in all its gory detail, is summarized in the Figure below, which follows Bryan et al. (2026) and a post from Thomas Lin Pedersen.