Take a look at Transcriber. This program generates time codes. If you were
recording continuously and knew the exact time you started recording you'd
be able to calculate the exact time at any point in the transcript based on
Transcriber's time codes.
Transcriber codes the transcript in XML. Aside from XML tags it also
generates XML tags for speakers and other qualities lexical events and the
newest version has something called named entities (which I haven't explored
much). You could probably modify these to your purposes. You could assign a
speaker tag to type of bird and some of the other tags, which you rename) to
bird locations and actions. It also allows you to write your own output
filters (assuming you are prepared to learn a little tcl scripting). This
would allow you to write script that would automatically calculate all the
times for you and output the details in a suitable format.
The latest version is 1.5.1 and is available here:
http://sourceforge.net/projects/trans/
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