While one can effectively train with heart rate there are some important considerations to be aware of. HR is not an absolute measurement like power. Rather it is a response to stimulus. HR will always lag from the beginning of any effort. So if you are doing say a 20 minute interval at 100% of threshold your HR may not reach that 100% level until several minutes in. When doing higher end intervals (Vo2 Max and Anaerobic Capacity) you will probably never reach the target HR before the end of the effort since they are short in duration.
It is VERY important to not try to reach the target HR too soon. The object is to keep the total effort at (in this example) threshold even throughout. Do not start out at 125% with the idea of getting up to 100% HR as soon as possible. The interval starts right away, not once you achieve the target HR.
So how do you know you doing the correct effort at the start? Unfortunately there is no easy answer. You must go by your perceived effort. Be cautious-the tendency is to start harder then you should be going. This hard start will be detrimental to the workout.
The ideal way to go is with a power meter. A power meter shows the correct targeted numbers immediately and eliminates the guesswork. This also helps you to avoid tapering off towards the end. The result is no wasted training time and precise intensity.
I am not trying to say that you cannot train effectively on HR alone. Just be aware of the limitations and be ready to use you perceived effort at the beginning of your interval efforts. If you have any questions feel free to contact me at firstname.lastname@example.org.