Generalizing 'collapse_mutationless_edges' and small fitchcount bugfix#181
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richardyz98 wants to merge 2 commits intomasterfrom
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Generalizing 'collapse_mutationless_edges' and small fitchcount bugfix#181richardyz98 wants to merge 2 commits intomasterfrom
richardyz98 wants to merge 2 commits intomasterfrom
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@@ Coverage Diff @@
## master #181 +/- ##
==========================================
- Coverage 87.40% 87.18% -0.23%
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Files 72 72
Lines 5631 5633 +2
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- Hits 4922 4911 -11
- Misses 709 722 +13
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This pull request includes the generalization of the
collapse_mutationless_edgesfunction. This allows us to use a function that does not factor in missing data when determining whether to collapse two nodes. If we do not collapse on missing data, then the baseline score increases for trees as missing data increases.Additionally, it fixes a small bug in fitchcount which can error if no root is provided, such as on an initial call of the function.