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Richard Parker has started to tolerate Pi on the tarpaulin when it is hot out, but Pi is tired of having to fear him, and decides it is time to impose himself and carve out his own territory.
To do this, Pi intentionally provokes Richard Parker to step into Pi’s territory, at which point he blows his whistle furiously and uses the raft to make the lifeboat go broadside - and thus rock uncomfortably for Richard Parker - so that the tiger will associate his nausea with the sound of the whistle. He allows Richard Parker to recover, then repeats the process until the whistle alone is enough to make the tiger retreat.
As Pi grows more carnivorous, he comes to realize that he must tame Richard Parker. He begins the training that he has devised so that he can have his own territory on the lifeboat and feel relatively safe there. Although it is not easy and is highly dangerous, he eventually manages to mark out his own territory and exert a certain amount of dominance over Richard Parker.
If you think about it, making a tiger experience nausea in an effort to keep yourself safe might be mean, but it won't hurt him.