For small tests, pre- and post-processing with R, you can start an interactive sessions on the login nodes. All other R jobs have to be submitted through the batch system. You can start an R job (inputfile.R) in batch mode with the following command:
bsub [LSF options] "R --vanilla --slave < inputfile.R > outputfile"
Here you need to replace [LSF options] with LSF parameters for the resource requirements of the job. Please find a documentation about the parameters of bsub on the corresponding wiki page about the batch system. In this case, stdout is redirected into "outputfile".