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To  compartmentalize your dog training means to take every behavior that you teach your dog, and break it down into as many separate behaviors as possible, all in order to create perfection in the performance of the finished behavior.  Compartmentalizing addresses all of the finer details of the exercise, and pieces them together carefully and methodically.  

Within our dog training, we are trying to avoid conflict as much as possible.  Conflict can come about in training when a dog is either refusing the behavior asked, or anticipating the behavior asked.  Although there are other elements of conflict, these two are the most common within dog training.  With compartmentalization, comes the ability to mark (marker training) and reward the dog at the precise moment within the complete exercise, as opposed to just rewarding the dog at the end of the completed exercise.
We also do not want the dog to get bored within the training, which can result in a lackluster performance.  By breaking exercises down and being able to address each fine point, you have the freedom to work on certain problem areas while putting other behaviors on the “back burner” for a bit.  
Coupled with marker training, using a compartmentalized approach to your dog training can also assist in creating a performance bursting with enthusiasm and integrity.  By breaking each exercise down, the dog ends up receiving many rewards for small jobs.  Think of it as your boss asking you to retrieve a file for him or her and upon delivery rewards you with a hundred dollar bonus.  Your level of motivation will immediately spike the next time he or she asks you to do some other small, seemingly meaningless task.
Later, you can vary the moments when you mark and reward, which will maintain the drive in the dog.  By varying your moments of mark and reward in training, the dog has a higher level of focus and commitment.  This is achieved by the dog not knowing when the mark is going to happen exactly, but yet still maintaining an anticipatory state of drive assuming the mark could happen in the next moment.
If we take heeling for example, the completed exercise itself can be broken down into several components.   Here are just a few of the components that you could potentially train separately.
: Head position (in place)
: Body position (in place)
: Forward movement 
: Backward movement 
: Left turns (in place)
: Right turns (in place)
: Left turns while moving
: Right turns while moving
These are literally just a few of the components needed to create beautiful heeling.  Once these pieces have been taught separately, you can then systematically chain them together, one behavior at a time,  moving step by step to the end goal: your finished heeling routine.  However, within this process, you always have the freedom and ability to maintain your drive and focus by going back and rewarding just one of the various pieces you have combined to create your finished behavior.      
When understood and implemented correctly, compartmentalization allows a trainer vast amounts of freedom within their dog training, and can develop a stellar performance in the dog.
Take care and safe training