fix some corrupted entries, deal with empty values

Signed-off-by: davharris <harry491@gmail.com>
Merge branch 'master' of https://github.com/NCEAS/commdyn

# By Eric Sokol
# Via Eric Sokol
* 'master' of https://github.com/NCEAS/commdyn:
  ERS edits to fish example -- script should now work with the directory architecture
  ERS edits to example to calculate diversity metrics for Bird data (BBS)