When the screen shakes it means that one of your Pokemon is poisoned and your HP is going down.
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it happens randomly like a critical hit, but pretty rare. You will know if you threw a critical ball if the ball shakes after the Pokemon is inside and it budges only once.
It means that you almost caught the Pokemon. It says that when you have two shakes.
A rare Pokemon is on a honey tree when you see the tree shaking. (the more it shakes the rare the Pokemon )
use your poke radar in grass and when the grass shakes that's just a ordinary Pokemon but when the shakes and there is a bit of light that is a shiny Pokemon
You have to find a patch of grass that shakes on its own. Go to that patch of grass, you will find often find Audino or Pansage.