brokilon.ccd.domain package¶ Subpackages¶ brokilon.ccd.domain.sranges package Submodules brokilon.ccd.domain.sranges.sranges module AncestralSplit get_callsite() get_sranges_map() get_sranges_map_tree() prelabel_tree() Module contents brokilon.ccd.domain.topology package Submodules brokilon.ccd.domain.topology.ccd module calc_entropy() get_ccd_tree_bottom_up() get_clades() get_maps() get_tree_from_list_of_splits() get_tree_probability() sample_tree_from_ccd() brokilon.ccd.domain.topology.ccd0_attempt module expand() get_ccd0() get_map_tree() get_maps_full() get_tree_from_dict_of_splits() get_tree_probability() Module contents brokilon.ccd.domain.transmission package Submodules brokilon.ccd.domain.transmission.find_infectors module find_infector() find_infector_unknown() find_infector_with_data() brokilon.ccd.domain.transmission.io module read_breath_nexus() brokilon.ccd.domain.transmission.label_transmission_history module _label_all_nodes() _label_all_remaining_unknowns() _label_leaf_and_reachable_nodes() _label_top_infected_nodes() label_transmission_tree() brokilon.ccd.domain.transmission.transmission_ccd module TypeCCD _add_internal_clade() _add_leaf_clade() _build_tree_dict_from_clade_splits() _sanitize_transm_ancest() get_transmission_map_tree() get_transmission_maps() median_sample() sample_trees_from_transmission_ccd1() transmission_tree_from_dict_of_splits() brokilon.ccd.domain.transmission.transmission_ccd0 module compatible() expand_tccd0() get_map_tree() get_transmission_ccd0() get_tree_from_dict_of_splits() Module contents Submodules¶ brokilon.ccd.domain.phylogeography module _find_deme() get_all_trees_represented() get_geo_map() get_geo_map_tree() get_tree_from_dict_of_splits() sample_trees_from_geo_ccd() Module contents¶