brokilon.ccd.domain.phylogeography module

brokilon.ccd.domain.phylogeography._find_deme(node, geo_ann_str)

From the node find the nearest node below that is either a leaf or a binary node. This is to ignore nodes that are along edges with state changes between binary nodes of the tree. (Might be possible to summarize the number of changes at some point but not now!)

Parameters:

• node – A node in a tree

• geo_ann_str – The attribute name to return

Returns:

returns the value of the attribute of the nearest binary/leaf node

brokilon.ccd.domain.phylogeography.get_all_trees_represented(geo_ccd_map)

brokilon.ccd.domain.phylogeography.get_geo_map(trees, geo_ann_str, ccd_type=1)

brokilon.ccd.domain.phylogeography.get_geo_map_tree(geo_ccd_map, geo_ann_str, taxon_map=None, branch_length_map={}, clade_count_map=None)

brokilon.ccd.domain.phylogeography.get_tree_from_dict_of_splits(splits, geo_ann_str, geo_ccd_map, taxon_map=None, branch_length_map={})

brokilon.ccd.domain.phylogeography.sample_trees_from_geo_ccd(n_samples, geo_ccd_map, geo_ann_str, clade_count_map)