Robert Sheldon has a workaround for SQL Server R Services’s limitation of a single input data set:
Despite the ease with which you can run an R script, the sp_execute_external_script stored procedure has an important limitation. You can specify only one T-SQL query when calling the procedure. Of course, you can create a query that joins multiple tables, but this approach might not always work in your circumstances or might not be appropriate for the analytics you’re trying to perform. Fortunately, you can retrieve additional data directly within the R script.
In this article, we look at how to import data from a SQL Server table and from a .csv file. We also cover how to save data to a .csv file as well as insert that data into a SQL Server table. Being able to incorporate additional data sets or save data in different formats provides us with a great deal of flexibility when working with R Services and allows us to take even greater advantage of the many elements available to the R language for data analytics.
Another option is using the rodbc package to connect back to SQL Server to retrieve more data.