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Oh man. I really hate to say it, but with an abusive person in the house that will not change his ways, I seriously recommend finding someone else that can take care of the dog, especially one that can dedicate some time to solve the dog's separation anxiety issues, which it appears she has. It wouldn't be fair to keep the dog in that kind of a situation if your dad is physically abusive to her. Wait until you're on your own to take on the task of having another dog.

That pllluuss, the crate is now a negative environment, it's the place shes thrown when she's bad.

You can start by taking her outside and walking her as much as you possibly can. You need to 1.tire her out and 2. The more time she spends outside, the more she pees outside, the more you praise her for peeing outside, the faster shell learn not to pee inside, and the more time she spends outside, the less likely shell pee inside and get in trouble for it. If you see a mess try to clean it and don't tell your dad.

Do a few crate exercises and maybe ask your dad to put her outside but never in her crate. Start by feeding all her meals in her crate. Don't walk away right away, do your homework or whatever in sight. Praise her for being calm and if she starts to bark just walk away. When ur dad screams and she stops barking, run in and praise her for being calm. She might start barking again after u walk away, but a couple times of this she should start to understand.