Coalescent models

Coalescent models#

Coalescent models for simulating genealogies. Besides the standard Kingman coalescent, this module implements the beta coalescent and Dirac coalescent models.

class CoalescentModel[source]#

Bases: ABC

Abstract class for coalescent models.

class StandardCoalescent[source]#

Bases: CoalescentModel

Standard (Kingman) coalescent model. Refer to the Msprime docs for more information.

class BetaCoalescent(alpha: float, scale_time: bool = True)[source]#

Bases: MultipleMergerCoalescent

Beta coalescent model. Refer to the Msprime docs for more information.

__init__(alpha: float, scale_time: bool = True)[source]#

Initialize the beta coalescent model.

Parameters:

  • alpha (float) – The alpha parameter of the beta coalescent model.

  • scale_time (bool) – Whether to scale coalescence time as described in Msprime docs. If False, the timescale is set to N.

scale_time: bool#

Whether to scale coalescence time.

alpha: float#

The alpha parameter of the beta coalescent model.

class DiracCoalescent(psi: float, c: float, scale_time: bool = True)[source]#

Bases: MultipleMergerCoalescent

Dirac coalescent model. Refer to the Msprime docs for more information.

__init__(psi: float, c: float, scale_time: bool = True)[source]#

Initialize the Dirac coalescent model.

Parameters:

  • psi (float) – The fraction of the population replaced by offspring in one large reproduction event.

  • c (float) – The rate of potential multiple merger events.

  • scale_time (bool) – Whether to scale coalescence time as described in Msprime docs. If False, the timescale is set to N.

psi: float#

The fraction of the population replaced by offspring in one large reproduction event.

c: float#

The rate of potential multiple merger events.

scale_time: bool#

Whether to scale coalescence time.

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