Question about the winter cycling plan

I posted this response on the thread above but I have not gotten any replies. But I had a question about the winter cycling program the work out witht he heart rate monitor. any help would be appriciated.

Thank you for the winter plan it looks very good. I will be doing it with my HR monitor on my indoor trainer at home. I have one question regarding the plan.

Example not taken from the plan but it explains my question

When the plan calls for you to do a 20 min set alternating 30 secs at 100-110% of your threshold HR and then 30 secs at 60-70% of your THR. I understand what it wants you to do but It takes more than 30 secs for your HR to get up to 100% of Threshold and more that 30 secs to get down to 60 to 70%  How do you measure this? Cadence? MPH?