I use R under Windows on several machines.
I know you can set the working directory from within an R script, like this
setwd(\"C:/Documents and Setti
For Ubuntu:
Insert the following command into your .Rprofile file (usually in your home directory):
setwd(Sys.getenv("PWD"))
Now your default working directory will be whatever directory you launched R from. Keep in mind you can also set up default workspaces in different directories by saving your workspace image as .RData wherever you plan to launch R (startup sources .Rprofile before searching for .Rdata in the cwd).