You can start feeding her in the crate. Also giving her treats in there, like maybe a kong with peanut butter. She has to know thats it's not a punishment and good things happen in there. If you're folding laundry or watching tv, you can make her run a lot before you go in that room. Then give her a small treat and try to get her to take a nap in the crate while you're still in the room.
Meeko was a little difficult at first but he eased up after we started doing this and he loves his crate now. You should never put him in as a punishment though. It should be their little room. If Meeks get bored and even scared from thunder, he'll disappear into his crate.
Good luck!!!
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Jill, Meeko's Mom |