To my understanding, in Pathfinder, I have all Cleric spells available to me but in order to use them I have to prepare them first.
How many can I prepare?
Does it depend on my spell slots or can I prepare all of them but cast only 3?
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Each day, you can prepare a total number of spells as listed in the table, plus any bonus spells you get for a high Wisdom score.
For example, a 1st-level cleric with 18 Wisdom: the table says 1+1 first-level spell slots, which is to say 1 from the cleric list and 1 from one of his domains. He also gets a bonus first-level slot from his high Wisdom. So, ignoring his domain spell slot, he can prepare two spells that day.
That means he can prepare, for example, 1 use each of divine favor and magic weapon. Or he could prepare 2 uses of divine favor, or 2 uses of magic weapon. And the next day, it’s the same deal but could be any cleric spell or pair of cleric spells. But he has to choose how many of each to prepare each day.