RF distance

[jeromekelleher]

We want an implementation of RF distance to compare trees with equal sample sets.

Here's some code to compute RF distance using dendropy:

def dendropy_rf_distance(ds1, ds2):
    tns = dendropy.TaxonNamespace()
    tree1 = dendropy.Tree.get(
        data=pk.to_newick(ds1),
        schema="newick",
        taxon_namespace=tns)
    tree2 = dendropy.Tree.get(
        data=pk.to_newick(ds2),
        schema="newick",
        taxon_namespace=tns)
    tree1.encode_bipartitions()
    tree2.encode_bipartitions()
    return dendropy.calculate.treecompare.symmetric_difference(tree1, tree2)

[Billyzhang1229]

Implemented Unweighted Robinson-Foulds Distance using Python set operations

• Add rf_distance function with tests for distance metrics #21

Now working on an efficient Numba version

• Update _get_node_partition() using numba and numpy arrays  #25