Index

_

_add_internal_clade() (in module brokilon.ccd.domain.transmission.transmission_ccd) _add_leaf_clade() (in module brokilon.ccd.domain.transmission.transmission_ccd) _asdict() (brokilon.ccd.types.CladeSplitInfo method) _build_tree_dict_from_clade_splits() (in module brokilon.ccd.domain.transmission.transmission_ccd) _cast_to_int() (in module brokilon.core.read_nexus) _field_defaults (brokilon.ccd.types.CladeSplitInfo attribute) _fields (brokilon.ccd.types.CladeSplitInfo attribute) _find_deme() (in module brokilon.ccd.domain.phylogeography) _get_deme_clades() (in module brokilon.metrics.generalized_robinson_foulds) _get_features_string() (in module brokilon.core.tree) _iter_descendants_levelorder() (brokilon.core.tree.TreeNode method) _iter_descendants_postorder() (brokilon.core.tree.TreeNode method)

_iter_descendants_preorder() (brokilon.core.tree.TreeNode method) _label_all_nodes() (in module brokilon.ccd.domain.transmission.label_transmission_history) _label_all_remaining_unknowns() (in module brokilon.ccd.domain.transmission.label_transmission_history) _label_leaf_and_reachable_nodes() (in module brokilon.ccd.domain.transmission.label_transmission_history) _label_top_infected_nodes() (in module brokilon.ccd.domain.transmission.label_transmission_history) _make() (brokilon.ccd.types.CladeSplitInfo class method) _meta_label_nodes() (in module brokilon.core.read_nexus) _parse_extra_features() (in module brokilon.core.tree) _read_newick_from_string() (in module brokilon.core.tree) _read_node_data() (in module brokilon.core.tree) _replace() (brokilon.ccd.types.CladeSplitInfo method) _sanitize_transm_ancest() (in module brokilon.ccd.domain.transmission.transmission_ccd) _translate_nodes() (in module brokilon.core.tree)

A

add_child() (brokilon.core.tree.TreeNode method) add_feature() (brokilon.core.tree.TreeNode method) add_features() (brokilon.core.tree.TreeNode method)

ancestor (brokilon.ccd.domain.sranges.sranges.AncestralSplit attribute) ancestral_range (brokilon.ccd.clades.sranges.SRangesClade attribute) AncestralSplit (class in brokilon.ccd.domain.sranges.sranges) ANCESTRY (brokilon.ccd.domain.transmission.transmission_ccd.TypeCCD attribute)

B

BaseClade (class in brokilon.ccd.clades) (class in brokilon.ccd.clades.base) BLOCKS (brokilon.ccd.domain.transmission.transmission_ccd.TypeCCD attribute) brokilon module brokilon.ccd module brokilon.ccd.clades module brokilon.ccd.clades.base module brokilon.ccd.clades.deme module brokilon.ccd.clades.sranges module brokilon.ccd.clades.transmission_ancestry module brokilon.ccd.clades.transmission_block module brokilon.ccd.cli module brokilon.ccd.cli.breath_helper module brokilon.ccd.cli.ccd_map_cli module brokilon.ccd.cli.common_options module brokilon.ccd.cli.geography module brokilon.ccd.cli.transcope module brokilon.ccd.domain module brokilon.ccd.domain.phylogeography module brokilon.ccd.domain.sranges module brokilon.ccd.domain.sranges.sranges module brokilon.ccd.domain.topology module

brokilon.ccd.domain.topology.ccd module brokilon.ccd.domain.topology.ccd0_attempt module brokilon.ccd.domain.transmission module brokilon.ccd.domain.transmission.find_infectors module brokilon.ccd.domain.transmission.io module brokilon.ccd.domain.transmission.label_transmission_history module brokilon.ccd.domain.transmission.transmission_ccd module brokilon.ccd.domain.transmission.transmission_ccd0 module brokilon.ccd.types module brokilon.core module brokilon.core.read_nexus module brokilon.core.taxon_map_utils module brokilon.core.tree module brokilon.majority_rule_consensus module brokilon.majority_rule_consensus.cli module brokilon.majority_rule_consensus.majority_consensus module brokilon.metrics module brokilon.metrics.generalized_kendall_colijn module brokilon.metrics.generalized_robinson_foulds module brokilon.metrics.robinson_foulds module

C

calc_entropy() (in module brokilon.ccd.domain.topology.ccd) change_taxon_map() (in module brokilon.core.taxon_map_utils) children (brokilon.core.tree.TreeNode property) clade (brokilon.ccd.clades.base.BaseClade attribute) (brokilon.ccd.clades.BaseClade attribute)

CladeSplitInfo (class in brokilon.ccd.types) common_options() (in module brokilon.ccd.cli.common_options) compatible() (in module brokilon.ccd.domain.transmission.transmission_ccd0) compile_matchers() (in module brokilon.core.tree) count_trees_in_nexus() (in module brokilon.core.read_nexus)

D

DateExtractionError deme (brokilon.ccd.clades.deme.DemeClade attribute) (brokilon.ccd.clades.DemeClade attribute) deme_robinson_foulds() (in module brokilon.metrics.generalized_robinson_foulds)

deme_robinson_foulds_reference() (in module brokilon.metrics.generalized_robinson_foulds) DemeClade (class in brokilon.ccd.clades) (class in brokilon.ccd.clades.deme) descendant (brokilon.ccd.domain.sranges.sranges.AncestralSplit attribute)

E

expand() (in module brokilon.ccd.domain.topology.ccd0_attempt) expand_tccd0() (in module brokilon.ccd.domain.transmission.transmission_ccd0)

extract_date_from_label() (in module brokilon.ccd.cli.breath_helper) extract_edge_set() (in module brokilon.core.tree) extracting_data() (in module brokilon.ccd.cli.breath_helper)

F

find_infector() (in module brokilon.ccd.domain.transmission.find_infectors) find_infector_unknown() (in module brokilon.ccd.domain.transmission.find_infectors)

find_infector_with_data() (in module brokilon.ccd.domain.transmission.find_infectors) float_to_date() (in module brokilon.ccd.cli.breath_helper) format_node() (in module brokilon.core.tree)

G

get_all_trees_represented() (in module brokilon.ccd.domain.phylogeography) get_cached_content() (brokilon.core.tree.TreeNode method) get_callsite() (in module brokilon.ccd.clades.sranges) (in module brokilon.ccd.domain.sranges.sranges) get_ccd0() (in module brokilon.ccd.domain.topology.ccd0_attempt) get_ccd_tree_bottom_up() (in module brokilon.ccd.domain.topology.ccd) get_clades() (in module brokilon.ccd.domain.topology.ccd) get_common_ancestor() (brokilon.core.tree.TreeNode method) get_distance() (brokilon.core.tree.TreeNode method) get_geo_map() (in module brokilon.ccd.domain.phylogeography) get_geo_map_tree() (in module brokilon.ccd.domain.phylogeography) get_leaves() (brokilon.core.tree.TreeNode method) get_map_tree() (in module brokilon.ccd.domain.topology.ccd0_attempt) (in module brokilon.ccd.domain.transmission.transmission_ccd0) get_mapping_dict() (in module brokilon.core.taxon_map_utils)

get_maps() (in module brokilon.ccd.domain.topology.ccd) get_maps_full() (in module brokilon.ccd.domain.topology.ccd0_attempt) get_root_age_from_leafs() (in module brokilon.ccd.cli.breath_helper) get_root_age_with_date() (in module brokilon.ccd.cli.breath_helper) get_sranges_map() (in module brokilon.ccd.domain.sranges.sranges) get_sranges_map_tree() (in module brokilon.ccd.domain.sranges.sranges) get_transmission_ccd0() (in module brokilon.ccd.domain.transmission.transmission_ccd0) get_transmission_map_tree() (in module brokilon.ccd.domain.transmission.transmission_ccd) get_transmission_maps() (in module brokilon.ccd.domain.transmission.transmission_ccd) get_tree_from_dict_of_splits() (in module brokilon.ccd.domain.phylogeography) (in module brokilon.ccd.domain.topology.ccd0_attempt) (in module brokilon.ccd.domain.transmission.transmission_ccd0) get_tree_from_list_of_splits() (in module brokilon.ccd.domain.topology.ccd) get_tree_probability() (in module brokilon.ccd.domain.topology.ccd) (in module brokilon.ccd.domain.topology.ccd0_attempt) get_tree_root() (brokilon.core.tree.TreeNode method)

H

has_block (brokilon.ccd.clades.transmission_block.TransmissionBlockClade attribute) (brokilon.ccd.clades.TransmissionBlockClade attribute)

I

is_leaf() (brokilon.core.tree.TreeNode method) is_root() (brokilon.core.tree.TreeNode method) iter_descendants() (brokilon.core.tree.TreeNode method)

iter_leaves() (brokilon.core.tree.TreeNode method) iter_prepostorder() (brokilon.core.tree.TreeNode method) iter_search_nodes() (brokilon.core.tree.TreeNode method)

L

label_transmission_tree() (in module brokilon.ccd.domain.transmission.label_transmission_history)

M

median_sample() (in module brokilon.ccd.domain.transmission.transmission_ccd) module brokilon brokilon.ccd brokilon.ccd.clades brokilon.ccd.clades.base brokilon.ccd.clades.deme brokilon.ccd.clades.sranges brokilon.ccd.clades.transmission_ancestry brokilon.ccd.clades.transmission_block brokilon.ccd.cli brokilon.ccd.cli.breath_helper brokilon.ccd.cli.ccd_map_cli brokilon.ccd.cli.common_options brokilon.ccd.cli.geography brokilon.ccd.cli.transcope brokilon.ccd.domain brokilon.ccd.domain.phylogeography brokilon.ccd.domain.sranges brokilon.ccd.domain.sranges.sranges brokilon.ccd.domain.topology brokilon.ccd.domain.topology.ccd brokilon.ccd.domain.topology.ccd0_attempt brokilon.ccd.domain.transmission brokilon.ccd.domain.transmission.find_infectors brokilon.ccd.domain.transmission.io brokilon.ccd.domain.transmission.label_transmission_history brokilon.ccd.domain.transmission.transmission_ccd brokilon.ccd.domain.transmission.transmission_ccd0 brokilon.ccd.types brokilon.core brokilon.core.read_nexus brokilon.core.taxon_map_utils brokilon.core.tree brokilon.majority_rule_consensus brokilon.majority_rule_consensus.cli brokilon.majority_rule_consensus.majority_consensus brokilon.metrics brokilon.metrics.generalized_kendall_colijn brokilon.metrics.generalized_robinson_foulds brokilon.metrics.robinson_foulds

N

NewickError

P

phygeo_mrc() (in module brokilon.majority_rule_consensus.majority_consensus)

prelabel_tree() (in module brokilon.ccd.domain.sranges.sranges) prob (brokilon.ccd.types.CladeSplitInfo attribute)

R

read_breath_nexus() (in module brokilon.ccd.domain.transmission.io) read_newick() (in module brokilon.core.tree) read_nexus_trees() (in module brokilon.core.read_nexus)

regular_mrc() (in module brokilon.majority_rule_consensus.majority_consensus) robinson_foulds() (in module brokilon.metrics.robinson_foulds) robinson_foulds_ccd() (in module brokilon.metrics.robinson_foulds)

S

sample_tree_from_ccd() (in module brokilon.ccd.domain.topology.ccd) sample_trees_from_geo_ccd() (in module brokilon.ccd.domain.phylogeography) sample_trees_from_transmission_ccd1() (in module brokilon.ccd.domain.transmission.transmission_ccd) search_nodes() (brokilon.core.tree.TreeNode method)

source (brokilon.ccd.clades.sranges.SRangesClade attribute) (brokilon.ccd.domain.sranges.sranges.AncestralSplit attribute) split (brokilon.ccd.types.CladeSplitInfo attribute) SRangesClade (class in brokilon.ccd.clades.sranges) support (brokilon.core.tree.TreeNode property)

T

translate() (in module brokilon.ccd.cli.breath_helper) transm_ancest (brokilon.ccd.clades.transmission_ancestry.TransmissionAncestryClade attribute) (brokilon.ccd.clades.TransmissionAncestryClade attribute) transmission_mrc() (in module brokilon.majority_rule_consensus.majority_consensus) transmission_tree_from_dict_of_splits() (in module brokilon.ccd.domain.transmission.transmission_ccd) TransmissionAncestryClade (class in brokilon.ccd.clades) (class in brokilon.ccd.clades.transmission_ancestry)

TransmissionBlockClade (class in brokilon.ccd.clades) (class in brokilon.ccd.clades.transmission_block) traverse() (brokilon.core.tree.TreeNode method) Tree (in module brokilon.core.tree) TreeError TreeNode (class in brokilon.core.tree) TypeCCD (class in brokilon.ccd.domain.transmission.transmission_ccd)

U

up (brokilon.core.tree.TreeNode property)

V

validate_ccd_type() (in module brokilon.ccd.cli.common_options)

W

write() (brokilon.core.tree.TreeNode method)

write_newick() (in module brokilon.core.tree)