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For the analysis, a few seconds at beginning and end do not influence the result. This should be because the listeners are often less concentrated or may think artefacts like clicks etc are due to their playing equipment which is starting or stopping. Don't know if this is true or not. Perhaps there is another explanation too, but standards don't explain anything.
There was another objective tool based on the work of Frank Baumgarte, which EarGuy implemented and played with in the r3mix forums. It seemed to consistently show bad results at the beginning of an mp3 file. I don't know of any listening tests which confirm this effect, or what could explain it, but in the files I prepare for listening tests, I sidestep this problem (if it is a real effect) by duplicating the entire sample, and then by cutting it in half (choosing the second half, of course) for the final file.
[tangent]Interestingly, Fraunhofer's mp3enc codec will produce different artifacting depending on what signal went before, so it can be tricky to capture bad sections for this codec by excerpting sections of a song, and the method I use above will yield different results for mp3enc than just using the straight sample.[/tangent]
I also found early on that playing files which don't begin or end with silence can cause clicks initially upon playback. I avoid this problem by adding some silence before and after the sample.
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