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The formula for efficiency = (Transmission time) / (Transmission time + 2*(Propagation time)) for stop and wait protocol. Reference
Can anybody tell why Transmission time is in the numerator because after all it is also a kind of delay we don't want. So how is it possible that increasing transmission time will increase efficiency of my network?

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It's a confusion in words used, the efficency is the latency compared to transmission time. Having a second of latency is less problematic if you have to transfert a large file (3 seconds) than a single data.

Remeber that your transmission time is constant and your latency have to be very small in comparison of your transmission time

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Efficiency is the amount of time spent transmitting as opposed to travel time (propagation).

Transmitting time is not changing but we want to calculate how much of the total time for transportation is spent doing the "necessary" work, which is the transmitting part. In an ideal world, the propagation time becomes so small that the fraction converges on 1.0. In the opposite world, like say transmitting to Mars, propagation time will be massive, and "efficiency" will converge on 0.0 (but obviously not reach it).

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