Encounters in the Safari zone differ from normal random battles. Instead of fighting, you can throw bait and rocks. Bait makes the Pokemon eat, which presumably makes it less likely to flee. The result of throwing rocks is making the opponent angry. Is there some benefit to them being angry?
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Prof. Rex did some in-depth research on this topic. You could try running his program with some sequences involving rocks and see if you can beat straight-up throwing safari balls vs. pokes with low flee rate (the 25, 50 rate mons). – aphid Nov 15 '21 at 08:36
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According to a couple of guides (here and here), there is a benefit to throwing rocks and making the Pokémon angry. It functionality works opposite to throwing bait.
When throwing bait, it makes the Pokémon more likely to stay, but makes it more difficult to catch.
When throwing rocks, it makes the Pokémon more likely to run away, but makes it easier to catch.
Wondercricket
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2No need to go for forum posts. Bulbapedia has the full algorithm. https://bulbapedia.bulbagarden.net/wiki/Kanto_Safari_Zone#Safari_Game – J. Mini Nov 13 '21 at 18:20
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@J.Mini (Facepalm) I always check Bulbapedia or Serebii first. Not sure why I didn’t this time – Wondercricket Nov 13 '21 at 20:53