brokilon.ccd.domain.transmission.find_infectors module

Module contains functions regarding the computation and plotting of WIW networks for transmission trees and transmission CCDs.

brokilon.ccd.domain.transmission.find_infectors.find_infector(node, indirect: bool = False)

Takes a node in a transmission annotated phylogenetic tree and returns its infector.

Parameters:

• indirect – Infer indirect transmissions, i.e. find last known infector

• node – Node of which to find the infector.

Returns:

Infector of node

brokilon.ccd.domain.transmission.find_infectors.find_infector_unknown(cur_u_node, root_node)

Finds the infector of nodes that are unknown, not leafs

Parameters:

• cur_u_node – A node whose transm_ancest is unknown

• root_node – The root node of a tree (tree.get_tree_root())

Returns:

brokilon.ccd.domain.transmission.find_infectors.find_infector_with_data(node, root_node, indirect: bool = False)

Finds the infector with extra data: distance to root of start and end of infection

Parameters:

• node – The node to find the infector of, in this case assumes to be a leaf

• root_node – The root node object of a tree (tree.get_tree_root())

• indirect – Currently not supported?

Returns: