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Add unweighted_rf_distance (symmetric_distance) function and tests #2643
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #2643 +/- ##
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- Coverage 89.72% 86.96% -2.77%
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Files 29 11 -18
Lines 31581 24358 -7223
Branches 6118 4501 -1617
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- Hits 28336 21182 -7154
+ Misses 1853 1817 -36
+ Partials 1392 1359 -33
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@Billyzhang1229 The docs error here is fixed in |
@benjeffery Thank you so much! I think I could do the rebase part. But I have question about the coverage report, the report shows some decrease for the files that I didn't change, do I need to worry about it? |
codecov has been pretty unreliable in reporting numbers. The comments on the PR are usually good. I'll double check this before merge, so don't worry about it. |
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This looks great @Billyzhang1229, thanks! I think the main thing we need here is a bit more testing to reassure ourselves that what we're computing is the same as what'd get using existing methods. How about a small simulation based test like:
Other than that, we just need to think about the naming and be a bit more precise about the documentation - but I think myself and @hyanwong can help with that. @hyanwong - thoughts about function naming here? |
@jeromekelleher Thanks for the feedback! I agree that additional testing would be beneficial to ensure the accuracy of our computations. NamingI am currently using I'm not sure which one is better for naming. So I just wrapped the def unweighted_rf_distance(self, other):
return self.symmetric_distance(other) In the future, we may also want to consider adding a If there is anything else you would like me to add or change, please let me know. |
I think I don't think We will need to be quite precise about what we're computing here in the documentation, but I can do that in a follow-on commit. |
I agree with Jerome. |
In fact, if we want to, we could allow the |
I don't see much point in this - it's forward compatible by not having the argument and we don't need it for this PR. |
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Sorry that we haven't got around to merging this yet @Billyzhang1229. It would be great to get this in, and I see you've added extra tests. Do you know how this performs in the case of trees with polytomies? There's an interesting publication at https://onlinelibrary.wiley.com/doi/full/10.1111/cla.12540 that sounds like it might give some useful pointers in this case. |
@mergify rebase |
✅ Branch has been successfully rebased |
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@Mergifyio rebase |
Add more tests using other existing package
✅ Branch has been successfully rebased |
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Add Unweighted Robinson–Foulds Distance (symmetric difference of two trees) function with tests
See also: