fix for move to reshape2, also drop plyr
fixup a couple of things that got munged in recent merge
missed one change that got munged
fixup to account for move to reshape2
fixup to account for move to reshape2, plus some bug fixes. Needs work...
update documentation
Forgot to add the data files to the Collate list.

Added taxon.table.R and translate.table.R to the Collate list in
DESCRIPTION.