Olá, pessoal! Boa tarde!
Uma ideia é entrar com múltiplos comandos para os argumentos e acionar o script com source().
###
C:\Program Files\R\R-2.15.3\bin>echo print(a+b) > script.R
C:\Program Files\R\R-2.15.3\bin>type script.R
print(a+b)
C:\Program Files\R\R-2.15.3\bin>R -e "a=2; b=3; source('script.R')
R version 2.15.3 (2013-03-01) -- "Security Blanket"
Copyright (C) 2013 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> a=2; b=3; source('script.R')
[1] 5
>
>
C:\Program Files\R\R-2.15.3\bin>