Kendall tau method added to mantel computation

[AnnaTruzzi]

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[AnnaTruzzi]

In Khaligh-Razavi, S. M., & Kriegeskorte, N. (2014) it is suggested to prefer the Kendall's tau over Spearman's rho as correlation coefficient when comparing models in which the order of variables is important. This is for example the case in y work where I am comparing deep neural networks embeddings with brain neural patterns.
Within this pull request I have minimally modified the _mantel.py function to add the Kendall's tau as one of the possible correlation methods.

Reference:
Khaligh-Razavi, S. M., & Kriegeskorte, N. (2014). Deep supervised, but not unsupervised, models may explain IT cortical representation. PLoS computational biology, 10(11), e1003915.

[ElDeveloper]

Thanks for the contribution @AnnaTruzzi, looks like there are conflicts with your branch. Also, would you mind adding a new test to exercise this choice?

[AnnaTruzzi]

Hi, I resolved the conflict, sorry about that.
In the _mantel.py function I already added the Kendall tau test, are you referring to a different one?

[ElDeveloper]

Thanks @AnnaTruzzi, really appreciate this. I was referring to adding a unit test in skbio/stats/distance/tests/test_mantel.py.

[AnnaTruzzi]

Hi,
I am not sure about what unit test is required, I'm sorry. And I do not want to mess everything up so I'll ask you first.
Would that be enough to add 'kendalltau' method in line 62 ot the test_mantel.py script so that it becomes as follows:
self.methods = ('pearson', 'spearman','kendalltau').

[ElDeveloper]

@AnnaTruzzi No need to worry about messing anything. Yes, you are correct we would need to add the method in that line as well as checking that the methods using that attribute also work. For example in line 99 and in line 183.

If you would like some pointers, here's a document where we give some suggestions on how to test your code.

[AnnaTruzzi]

Added and ran in the debugger: the 39 tests ran were ok.
It did throw some warnings but not because of the kendalltau method. They were already there previously to my addition.
Since I am not sure whether they are relevant to you or for my pull request, I'll copy and paste them here:

• scipy/stats/stats.py:3399: PearsonRConstantInputWarning: An input array is constant; the correlation coefficent is not defined.
  warnings.warn(PearsonRConstantInputWarning())

• numpy/lib/function_base.py:2534: RuntimeWarning: invalid value encountered in true_divide
  c /= stddev[:, None]

• scipy/stats/_distn_infrastructure.py:901: RuntimeWarning: invalid value encountered in greater
  return (a < x) & (x < b)

• scipy/stats/_distn_infrastructure.py:901: RuntimeWarning: invalid value encountered in less
  return (a < x) & (x < b)

• scipy/stats/_distn_infrastructure.py:1892: RuntimeWarning: invalid value encountered in less_equal
  cond2 = cond0 & (x <= _a)

[ElDeveloper]

Thanks for adding tests, I've left a few comments in the PR.

[ElDeveloper]

@AnnaTruzzi, one more note: you'll need to resolve conflicts in the CHANGELOG.md file. Let me know if I can help.

[AnnaTruzzi]

Hi, thank you for correcting the mistakes!
I applied all the requested changes and resolved the conflict in the changelog file.

[ElDeveloper]

@AnnaTruzzi thanks for updating the PR. I just noticed the entries in the CHANGELOG.md file are in a section for an older release. Also, going through the test_mantel.py, I've noticed that there's a few other test cases that would be good to test. For example adding a check for 'kendalltau' in the method in line 88 test_statistic_same_across_alternatives_and_permutations, and the method in line 112 test_zero_permutations.

Apologies for not catching this before, thanks so much for your contribution.

[AnnaTruzzi]

Hi, sorry for the later reply, I've been caught in some deadlines.
I fixed the CHANGELOG file and added the two tests you asked for
Let me know if I can do anything else!

[AnnaTruzzi]

Hi @ElDeveloper, do I need to make other changes for this pull request?
Let me know, thank you!

[ElDeveloper]

Hi @AnnaTruzzi, thanks for following up. The code changes look good, however I think the conflict resolution in the ChangeLog is still not correct. The diff still shows a few more bullet points that shouldn't be included in your PR. Can you fix that? The diff should only show * Added Kendall Tau as possible correlation .... Let me know if I can help somehow! 👍

[AnnaTruzzi]

Hi! yes at this point I could use some help, I guess I'm missing some fundamental step. What I do to to solve the conflict is to open the changelog with the conflicting lines, and remove the two versions leaving only the right line and then I commit it. What am I doing wrong? Thank you!

[ElDeveloper]

Nothing wrong per se, I think it might be just due to git's confusing nature 😆. I think you might be able to solve this if you edit the CHANGELOG.md file and remove lines 49, 48, 47, 46 and 15.

[AnnaTruzzi]

Thank you! Lines deleted

[ElDeveloper]

Thanks so much!