Add Hommola cospeciation test

Here, we have added a statistical test for host:parasite cospeciation derived from Hommola et al (2009, Molecular Biology and Evolution). This is added as a new module called evolve under math.stats.

We are looking for feedback on the organization and naming of the evolve module. We're not quite sure what to add to the top level description for this module, so any other ideas would be appreciated. 

Note: the test itself is using numpy arrays rather than distance matrix objects because we are using the positional relationships between host, parasite, and an interaction matrix rather than the labels. 
I believe there was also some issue with the fact that we haven't ported the script that calls this in QIIME over from cogent to skbio yet -- since we are generating one of these DMs from an alignment via cogent, it would ease things on that side if we could pass the lower level Numpy array rather than convert to an skbio DM object. 


-j
—
Sent from Mailbox

On Wed, Aug 6, 2014 at 4:35 PM, Yoshiki Vázquez Baeza
<notifications@github.com> wrote:

>> +
>> +    p_val = (below + 1) / (permutations + 1)
>> +
>> +    return p_val, r, perm_stats
>> +
>> +
>> +def _get_dist(labels, dists, index):
>> +    """Function for picking a subset of pairwise distances from a distance
>> +    matrix according to a set of (randomizable) indices.
>> +    Derived from Hommola et al R code
>> +
>> +    Parameters
>> +    ----------
>> +    labels : list of strings
>> +        names associated with pairwise distance matrix
>> +    dists : numpy.array
> @tanaes, @nbresnick and I talked about this but we were not sure about whether we should use a DM object as the labels of the ids themselves are never used and the code really only operates on the data matrices themselves.
> ---
> Reply to this email directly or view it on GitHub:
> https://github.com/biocore/scikit-bio/pull/557/files#r15901563