Unix

• screen: This allows you to do multiple 'windows' on unix. If you are running R interactively, you probably want to do it via screen, because it allows you to exit the R session, go back to the unix terminal, and then re-enter R -- and from any connection. You can log-off at the department and log-back on at home and still re-enter your R session. However, the rule above still applied. Don't keep a R session running longer than a day without really good reason.

• makefiles This is very useful for automating a series of steps. For example, I always create a make file that will compile my knitr file or latex file. For extensive simulations or processing of data, especially that have dependencies (if file X updates, you need to rerun command A, but otherwise don't), you can code in the dependencies in makefile, and make will only rerun if neeed. Knitr caching does this to some degree, but I find it much trickier -- I always wind up 'forcing' it to rerun something or being frustrated that it reran something I didn't think changed.

  Snakemake Is a more recent tool that helps make it easy to create make workflows

Back to top