I have a bunch of R scripts which I am running on a Windows machine and want to ensure that the code remains unread by those not intended to see it. On a Linux box, I could
I don't think this is possible because the R interpreter has to be able to decrypt and read the code in order to execute it which means that whoever is using that interpreter will also be able to decrypt and read the code.
I am by no means an expert, so I reserve the right to be 100% wrong about that statement.
I believe the best solution is to ensure value comes from the expertise and services provided by your company and it's employers---not from keeping secrets.
Failing that, you could try separating the code into a client/server model. That way the client just sends data and receives results---they never have access to the code that runs on the server.
However, the scientist in me just said "that solution sucks and I would never trust results provided under such conditions".