tracts.phase_type_distribution.PhTMonoecious

class PhTMonoecious(migration_matrix, rho=1)

Bases: PhaseTypeDistribution

A subclass of PhaseTypeDistribution providing the specific Phase-Type tools for the Monoecious Markov approximation.

migration_matrix

The migration matrix given as input without contributions at generations 0 and 1.

Type:

npt.ArrayLike

num_populations

The number of populations considered in the demographic model.

Type:

int

num_generations

The number of generations considered in the demographic model.

Type:

int

t0_proportions

The total contribution from each ancestral population. Corresponds to Eq. (EQ) in the manuscript.

Type:

npt.ArrayLike

full_transition_matrix

The intensity matrix S^M of the Monoecious Markov Model. Corresponds to Eq. (EQ) in the manuscript.

Type:

npt.ArrayLike

equilibrium_distribution

The equilibrium distribution of the Monoecious Markov Model. Corresponds to Eq. (EQ) in the manuscript.

Type:

npt.ArrayLike

alpha_list

A list containing, for each ancestral population p, the initial state of the Phase-Type distribution for the tract length of population p. Correspond to Eq. (EQ) in the manuscript.

Type:

list

transition_matrices

A list containing, for each ancestral population p, the submatrix of full_transition_matrix corresponding to transitions within p. It is used to compute the distribution of tract lengths from population p.

Type:

list

S0_list

A list containing the sum across columns of every transition matrix in transition_matrices.

Type:

list

inverse_S0_list

A list containing the sum across columns of the inverse of every transition matrix in transition_matrices.

Type:

list

Parameters:

• migration_matrix (npt.ArrayLike) – An array containing the migration proportions from a discrete number of populations over the last generations. Each row is a time, each column is a population. Row zero corresponds to the current generation. The migration rate at the last generation (migration_matrix[-1,:]) is the “founding generation” and should sum up to 1.

• rho (float, default 1) – The recombination rate (positive real number).

Notes

Non-listed attributes are for internal use only.