Here's a test calculation sheet.
It's the "stack loss method". If you have a known fuel, of known moisture content, you can calculate combustion efficiency and heat transfer efficiency by measuring 6 things: weight of the fuel load, room temperature, Flue gas; temperature, CO concentration, CO2 Concentration, and O2 Concentration.
Really you're not actually measuring how much heat the stove releases to the room, instead you calculate how much heat the wood produces (known fuel, moisture content, and weight consumed (flue gas composition ties in here to calculate combustion efficiency)), and how much heat leaves through the flue, temperature and flue gas concentrations.