It is likely behavioral right now. And no wonder, given all she has likely been through, but it IS solvable!
When you take her out, be prepared to stay outside until she does something, then praise, praise, praise!
You can skip the "rubbing nose in it," as that is not gonna penetrate.
What you do need to do first off is get a good cleaner that will eliminate the enzymes that tell a dog "good spot to pee here!" - there's one in stores here called "Nature's Miracle" that does the job well.
Is she being crate-trained at all? That's something to consider as well, as a healthy dog will NOT mess where it sleeps.
Sorry so many questions, and I am sorry that the shelter was not more forthcoming with information on the poor girl. How old is she?
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