I have seen several breakdown and rough rules for adjusting a monster's CR according to various special abilities and qualities. The Pathfinder Core book and Bestiary has rules about things like high and low damage, ability scores, and the bones of the process, but I am looking for more information about things like;
- Damage Reduction
- Breath Weapons
- Spell like abilities & caster level
- Weaknesses like vulnerability to fire
- Special Attacks
- Fly, swim, and burrow speeds
I have a solid understanding of what challenges this represent, and mostly adjust a monster's CR by ear, but I know I've seen several rough and ready rules for this.