I've noticed that when I bake cupcakes, they come out of the oven just fine.  I let them cool in the pan and before I know it, the cupcakes shrink so they are not they nice full size they were when they came out of the oven.  Does anyone have any idea why the cupcakes would do this?  I bake vegan cupcakes from the Vegan Cupcakes Take Over the World cookbook.

A possibility could that you left them in the pan to cool. The pan is still hot so it'll continue to bake the cupcakes, but I wouldn't take my word for it I'm not a professional. Just thought I would my idea.

Dee is right. Dump those cupcakes out of the pan as soon as they come out of the oven. When I first started baking I had this problem and haven't since I've started getting them out of the pan as soon as they're done, so they can cool on a baking sheet/rack.

When I bake cupcakes and muffins, I always let them cool in the pan and there's no shrinkage. So you might be over-baking your cupcakes. Remove them from the oven when they are done. Then leave them to cool in the tin.