brokilon.ccd.clades package

Submodules

• brokilon.ccd.clades.base module
  • BaseClade
    • BaseClade.clade
• brokilon.ccd.clades.deme module
  • DemeClade
    • DemeClade.deme
• brokilon.ccd.clades.sranges module
  • SRangesClade
    • SRangesClade.ancestral_range
    • SRangesClade.source
  • get_callsite()
• brokilon.ccd.clades.transmission_ancestry module
  • TransmissionAncestryClade
    • TransmissionAncestryClade.transm_ancest
• brokilon.ccd.clades.transmission_block module
  • TransmissionBlockClade
    • TransmissionBlockClade.has_block

Module contents

class brokilon.ccd.clades.BaseClade(clade: frozenset)

Bases: object

Base class representing a clade — a set of taxa/leaves.

Attributes:

clade (frozenset): A frozen set of taxa or node labels in this clade.

clade: frozenset

class brokilon.ccd.clades.DemeClade(clade: frozenset, deme: str)

Bases: BaseClade

Clade with a compartment annotation (deme) that indicates a location or similar

Attributes:

deme (string): Indicates a compartment this clade belongs to.

deme: str

class brokilon.ccd.clades.TransmissionAncestryClade(clade: frozenset, transm_ancest: str)

Bases: BaseClade

Clade with transmission ancestor, i.e. who infected this clade.

Attributes:

transm_ancest (str): Transmission ancestor

transm_ancest: str

class brokilon.ccd.clades.TransmissionBlockClade(clade: frozenset, has_block: bool)

Bases: BaseClade

Clade with a flag indicating whether a transmission block (event) occurred on the edge.

Attributes:

has_block (bool): Whether this clade was preceded by a block of transmissions.

has_block: bool