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Believe it or not, all undiapered babies will do that, not just your rat. I think you will need to wait it out. I am not sure you can toilet train a rat or not but if you can, here is the process used for dogs. Feed the animal and keep it in a cage continuously. When you let the animal out, place it first in the spot where you want it to train and wait for the inevitable. If the animal "goes," then praise it highly and give it a treat. Then place it back in its cage. Continue until the animal understand what the treat is for.
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