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Pivots of any kind are a hint that you should have used a database from the start.
While importing into SQL Server you should normalize your data model (each field should depend on the key, the whole key and nothing but the key) then add appropriate indexing.
If you use SQL Server 2016, that has R built-in.
A slightly technical question on Power Query/Power Pivot.
We get big csv files, 10,000,000 rows plus, and point PowerPivot at them and do the manipulation in PowerPivot.
Would there be any performance improvement in importing the csv into SQL server and then pointing PowerPivot at that?