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At the time domain, the amplitude of the sound waveform is the absolute deviation from the zero, which can be estimated by the root mean square (RMS) of the signal. Of course, determining the zero baseline (silence) is important, but calibration it is not always an issue while recording animal vocalization recording, and usually we care about the relative intensity of the sound, which is estimated at the frequency domain in units deciBels dB
where Pf is the power at any one frequency and were baseline is (arbitrarily) set to 70dB as a default.

Amplitude is measured in dB scale, but note that the power is un-scaled, hence the baseline is arbitrary. You can adjust the baseline value in options->feature calculation->amplitude baseline. SAPII uses amplitude as one of the criteria for segmenting syllables and adjustments are based on relative values (namely, you adjust the amplitude slider to be slightly above the cage noise observed in the spectral image). Other than that, however, amplitude is not used for any other procedure.