Flow efficiency is a measure of how much of the overall lead time is due to waiting time: Lead Time = Value Work Time + Waiting Time
Most kanban systems separate the waiting from the doing and calculating the overall wait time is a matter of summing up all the wait times.
Here is an example Kanban visualisation of the value flow the total time in all the wait states: (Waiting for Develop + Waiting for Test + Waiting for Deploy)
The total work time: (In Develop + In Test + Deploy)
Kanban System Lead Time = Total wait time + Total work time
Flow Efficiency = (In Develop + In Test + Deploy)/Kanban system lead time
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