BUG/ENH/DOC: Change arguments named id_ to id

Making a quick test in IPython, it turns out that there's no need to
have the variables named id_ as these won't shadow the built-in function
`id` anywhere but inside the methods, which is fine as right now having
these arguments superseded by an underscore is generating Sphinx
warnings, see this example:

(skbio)yoshikivazquezbaeza:~$ ipython
Python 2.7.6 (v2.7.6:3a1db0d2747e, Nov 10 2013, 00:42:54)
Type "copyright", "credits" or "license" for more information.

IPython 2.0.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

In [1]: def foonction(id='x'):
   ...:     print id
   ...:

In [2]: foonction()
x

In [3]: id(foonction)
Out[3]: 4363449240