A Personnel Calculation Rule (pcr) is made up of Operations, and it is called by a Function.
Use t-code pe04 to look at them, at how they are built, at their source code, etc.
A Custom Function or a Custom Operation can be created by an ABAP programmer, and are "Custom Programs" called while processing a Schema (once the Custom Function is inserted into the Schema, or the Custom Operation is inserted in a pcr that is in the Schema).