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