tracts.hybrid_pedigree

This module implements the hybrid pedigree model for tract length distributions. It computes a mixture of Phase-Type distributions, each describing the tract length distribution conditioned on a pedigree structure. Dioecious admixture is considered on a finite chromosome.

See Appendix E of the manuscript for details on the model and the implementation.

Functions

HP_loglik(mig_matrix_f, mig_matrix_m, rr_f, ...)	Calculates the maximum-likelihood in a Poisson Random Field.
HP_tract_length_histogram_multi_windowed(...)	Calculates the tract length histogram on multiple chromosomes of lengths chrom_lengths.
all_possible_trees_as_arrays(T, N[, mig_at_last])
density_hybrid_pedigree(which_migration, ...)
generate_trees(current_gen, max_gen, N[, ...])
get_pedigree(T)
hybrid_pedigree_distribution(mig_matrix_f, ...)	This function computes the tract length distribution as a Phase-Type density or histogram on a finite chromosome of length L, using the Hybrid-Pedigree model.
prob_of_pop_setting(ms, ...)
tree_to_array(tree, max_nodes)	Convert a tree to its array representation.