Kevin,

The inst/ directory gives a good handle to pass arbitrary directory layouts
of your choosing through.  You just need to avoid inst/data as it would clash
with an existing data/ directory.

I think I have seen

    inst/rawData
    inst/extData                # as in 'external data'

and of course

    inst/scripts

or

    inst/tools

Note that there is a reasonable discussion in Writing R Extensions, but as
always, you have to find it first.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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