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A little update as it might be useful for other users.
Neal's answer made sense the way he presented it. However, it didn't quite add up with the data I had. To find out what the calculation is in both cases, I generated hourly reports in both eQUEST and EnergyPlus. Here is what I found out:
Here is an excerpt from an hourly report from eQUEST that illustrate the calculation:
In this example, the total furnace capacity is 39988 Btu/h and the rated HIR is 1.25.
Here is an excerpt from an hourly report from EnergyPlus that illustrate the calculation:
In this example, the total furnace capacity is 39988 Btu/h and the rated HIR is 1.25.
Then, if we look at (eq. 1) and (eq. 2):
In conclusion PLF and HIR f(PLR) are not quite the same.
Using this relation I converted the curve used in eQUEST (by default) to the match the PLF used in EnergyPlus.