Jukes cantor likelihood #73
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beginning binary tree counting streamline a few tests and use new test dag format and lint
| @@ -913,6 +805,19 @@ def test_node_support(): | |||
| assert is_close(exp(nd[node]), od[node], tol=0.0001) | |||
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| def test_conditional_annotation_nilpotent(): | |||
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This is a super fun test!
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Everything looks great! It might be good to incorporate a test that asserts likelihood implementations satisfy basic sanity tests, both to insure that and to formalize their function calls and so forth in case any calls change in future, but I don't think that is a necessary addition at this point
Can you remind me-- this is because it just didn't work well? |
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For now I've abandoned the idea because there doesn't seem to be a good way of counting bifurcating resolutions correctly, since the new nodes that would result from resolving a multifurcating node may already be in the DAG. I think there's something more involved that could be done that would involve changing the data structure slightly... |
This PR provides an implementation of Jukes Cantor likelihood on histories, with branch lengths inferred to match the expected number of mutations on each branch to the observed number of mutations on that branch.
Also included:
__contains__method so thathistory in dagreturns whetherhistoryis among the histories indag