As soon as the animal understand s what a given cue means, the cue, or positive discriminative stimulus, becomes in itself a conditioned positive reinforcer, like the click. Thus a cue can be used as a reinforcer for behavior that occurs as the cue is being given. One may for example use the well-established positive cue for one behavior to shape another behavior, or to reinforce previous behavior in a chain. The cue can be used also as marker signal, just as if it were a click, to pinpoint especially good aspects of another behavior. It seems likely, too, that the desirable emotional response that we know to be associated with the click also accompanies the presentation of these positively conditioned stimuli.
Behavior that has been trained by correction may also have associated discriminative stimuli, which indicate when the specific behavior is to occur. However, these discriminators, or commands, may or may not lead to positive reinforcement. If the animal fails to perform the behavior, or performs it incorrectly, the stimulus may lead to punishment (usually called 'correction'. The negative discriminative stimulus, usually called a command, is now a conditioned negative reinforcer, signaling the opportunity for avoiding punishment.
Even if the behavior was trained entirely with positive reinforcement, if one now clicks for correct behavior following a discriminator ( a cue, command, or signal) but also gives aversive correction (leash pop, verbal reprimand, etc.) for incorrect behavior following that same stimulus, the stimulus immediately loses its value as a positive reinforcer. It is, at best, ambiguous in terms of reinforcement. It is not a click. It no longer automatically triggers the positive emotions associated with conditioned positive reinforcers. It can no longer be predictably used inside a chain to reinforce previous behavior.