If you are installing a prehung door on hardwood, ceramic tile, linoleum, etc... the jambs (or frame)will sit on the floor. If carpet is going to be installed where the door is going, you should leave the jambs up off of the floor 3/8" to 1/2" to allow for the carpet to be tucked underneath the jambs and to prevent the door from dragging the carpet during use.

norespect,
by bare floor, do you mean subfloor or a finished wood floor or another material? You should allow for an additional 1/2 to 3/4"

Thanks for your answers.
Piffin,This is an unfinished basement with a concrete floor. Most areas will be carpeted except for the bathroom which will be tile then transition to carpet.