My parents had a dog like that. She would hide under the kitchen table and shake everytime there was lightning. Oddly enough, she did the same thing with camera flashes. I’m not sure if there’s tons you can do about it, but I would say that as she becomes more confident in you and in her surrounding and gets used to the rain she’ll relax a little. Maybe just giving her a safe cave to hide in during the rain when you’re not there will help her feel less exposed.