Perfect -- thank you for the suggestion. You helped me get past the fact that the script was dying on the second call to the module - no need to reinitialize R each time.

Now I have a new problem, although the program processes each site I still get the following error message for each site processed:
Calculating Stats on site: rs11245203...
Destroying R reference object `205253'
Destroying R reference object `205251'
Destroying R reference object `205252'
Error: could not find function "DESTROY"
Caught error in R::call()

I get statistical calculations for every site, however a memory leak exists that may cause problems with larger files.

Thank you for your help in getting me further, please let me know if you have any more suggestions.