Any Python programmers willing to help me find a bug?

I’m working on a Python script for my sister to help with her dissertation for her doctorate in marine biology. I’ve started a thread on dreamincode, but have been unable to pin down the source of the bug thus far. If you’re a Python coder, and have a bit of time to look through my amateurish code (the most recent, edited version is one of the later posts), I’d REALLY appreciate the help. It’s FOR SCIENCE!