do NPC class levels count as full CR when calculating encounters?
Example:
a lvl 1 adept = CR1
a lvl 3 warrior = CR3
Adding NPCs: Creatures whose Hit Dice are solely a factor of their class levels and not a feature of their race, such as all of the PC races detailed in Races, are factored into combats a little differently than normal monsters or monsters with class levels. A creature that possesses class levels, but does not have any racial Hit Dice, is factored in as a creature with a CR equal to its class levels –1. A creature that only possesses non-player class levels (such as a warrior or adept) is factored in as a creature with a CR equal to its class levels –2. If this reduction would reduce a creature's CR to below 1, its CR drops one step on the following progression for each step below 1 this reduction would make: 1/2, 1/3, 1/4, 1/6, 1/8.
just want to mention something else, can't find the rule but i think it's under equipping NPC's. Joana is correct but that is also for NPC's with level appropriate NPC gear. if the NPC has the equipment of a PC then his CR can be increased by 1, and if he has no or limited equipment than his CR would be -1 lower.
NPC Gear Adjustments: You can significantly increase or decrease the power level of an NPC with class levels by adjusting the NPC's gear. The combined value of an NPC's gear is given in Creating NPCs on Table: NPC Gear. A classed NPC encountered with no gear should have his CR reduced by 1 (provided that loss of gear actually hampers the NPC), while a classed NPC that instead has gear equivalent to that of a PC (as listed on Table: Character Wealth by Level) has a CR of 1 higher than his actual CR. Be careful awarding NPCs this extra gear, though—especially at high levels, where you can blow out your entire adventure's treasure budget in one fell swoop!
I would also recommend to look closely at the CRs of commoner NPCs. In some cases, having the CR lowered by another notch might be called for. Your average 1st level commoner can count himself lucky if he has a +1 on anything besides two skills, if he has average attributes.
i normally change NPC CRs to "starting at CR 1/2, every NPC level increases the CR by half a step and every PC level by 1 step" mostly because i use a 20 point buy and at 9th level, a level 9 "NPC warrior" is NOT a CR 7, its more like a CR 5 if that.
so a level 10 NPC warrior would be a CR 5, and with NPC loot they are tanky but don't do all that much damage for a smart party that denies flanking.