skbio.core.tree.TreeNode.compare_rfd¶

TreeNode.compare_rfd(other, proportion=False)[source]¶

Calculates the Robinson and Foulds symmetric difference

Parameters:	other : TreeNode A tree to compare against proportion : bool Return a proportional difference
Returns:	float The distance between the trees
Raises:	ValueError If the tip names between self and other are equal.

See also

compare_subsets, compare_tip_distances

Notes

Implementation based off of code by Julia Goodrich. The original description of the algorithm can be found in [R25].

References

[R25]

(1, 2) Comparison of phylogenetic trees. Robinson and Foulds. Mathematical Biosciences. 1981. 53:131-141

Examples

>>> from skbio.core.tree import TreeNode
>>> tree1 = TreeNode.from_newick("((a,b),(c,d));")
>>> tree2 = TreeNode.from_newick("(((a,b),c),d);")
>>> tree1.compare_rfd(tree2)
2.0