tracts.phase_type.hybrid_pedigree

Hybrid-pedigree refinements (H-DC, H-DF) of the Dioecious phase-type approximations: enumerates the possible migration settings over a fixed-depth pedigree and averages PhTDioecious predictions over them, weighted by their probability under the model. Entry points are density_hybrid_pedigree()/hybrid_pedigree_distribution() (tract length density), HP_tract_length_histogram_multi_windowed() (binned histogram, used by tracts.driver_utils) and HP_loglik() (log-likelihood).

Functions

HP_loglik(mig_matrix_f, mig_matrix_m, rho_f, ...)	Calculates the maximum-likelihood in a Poisson Random Field, when admixture is modelled using the hybrid-pedigree refinement of the DC or DF models.
HP_tract_length_histogram_multi_windowed(...)	Calculates the tract length histogram for the hybrid-pedigree refinement of the DC or DF model for multiple chromosome lengths.
all_possible_trees_as_arrays(T, N[, mig_at_last])	Generates all possible trees representing the migration settings in a pedigree of T generations with N ancestral populations.
density_hybrid_pedigree(which_migration, ...)	Computes the tract length density or histogram for a given pedigree configuration, as specified by the which_migration-th element of migration_list, using the Hybrid-Pedigree refinement of the DC or DF model.
generate_trees(current_gen, max_gen, N[, ...])	Recursively generates all possible binary trees representing the migration settings in a pedigree of max_gen generations.
get_pedigree(T)	Generates a matrix representing a pedigree structure of a given number of generation.
hybrid_pedigree_distribution(mig_matrix_f, ...)	This function computes the tract length distribution as a Phase-type mixture on a finite chromosome of length L, using the Hybrid-Pedigree refinement of the DC or DF model.
prob_of_pop_setting(ms, ...)	Computes the probabily of a given configuration of migrant ancestors in the pedigree, as specified by the ms-th element of all_possible_migrations_list.
tree_to_array(tree, max_nodes)	Convert a tree to its array representation.