Did you take it and a fresh fecal specimen to a vet within 48 hours like you were suppose to?
I'd start there, and while there you may address any and all other concerns you may have.
It's not the dogs job to let you know when it needs to go out, it's yours, to provide proper scheduled feedings* and exercise/elimination times**.
Woo Hoo a full two weeks, you don't say!
Well have I got news for you, training requires a lot of patience, constant supervision, containment when you can't, immediate correction when caught in the act, consistency, diligence and time, minimum 6-18 months, if done properly, to start on your part.
Once trained you must still enforce what was taught on the daily basis, for the life of the dog, 12-17 years.
Stop shouting. Get rid of the pads, you're confusing her, she shouldn't be allowed to go indoors at all, only outside, no wonder you're having a problem.
Dogs have been trained for millenniums without a crate, this crate thing, seems to be fairly new as are those disgusting pads. Confine her to a small room with an easily cleanable floor.
I wish you luck as you're going to need it, you've got a long road ahead of you.
*
http://i40.photobucket.com/albums/e224/GLLNTKNIGHT/feeding_zps90a9666f.jpg
**
http://i40.photobucket.com/albums/e224/GLLNTKNIGHT/exercise1_zpsfb9dd351.jpg