int_get_trans_emiss module

itrails.int_get_trans_emiss.trans_emiss_calc_introgression(t_A, t_B, t_C, t_2, t_upper, t_out, t_m, N_AB, N_BC, N_ABC, r, m, n_int_AB, n_int_ABC, cut_AB, cut_ABC, tmp_path='./')[source]

This function calculates the emission and transition probabilities given a certain set of parameters.

Parameters:

  • t_A (numeric) – Time in generations from present to the first speciation event for species A (times mutation rate)

  • t_B (numeric) – Time in generations from present to the migration event for species B (times mutation rate)

  • t_C (numeric) – Time in generations from present to the migration event for species C (times mutation rate)

  • t_2 (numeric) – Time in generations from the first speciation event to the second speciation event (times mutation rate)

  • t_upper (numeric) – Time in generations between the end of the second-to-last interval and the third speciation event (times mutation rate)

  • t_out (numeric) – Time in generations from present to the third speciation event for species D, plus the divergence between the ancestor of D and the ancestor of A, B and C at the time of the third speciation event (times mutation rate)

  • t_m (numeric) – Time in generagions from admixture time until first speciation time

  • N_AB (numeric) – Effective population size between speciation events (times mutation rate) for AB

  • N_BC (numeric) – Effective population size between speciation events (times mutation rate) for BC

  • N_ABC (numeric) – Effective population size in deep coalescence, before the second speciation event (times mutation rate)

  • r (numeric) – Recombination rate per site per generation (divided by mutation rate)

  • m (numeric) – Migration rate (admixture proportion)

  • n_int_AB (integer) – Number of discretized time intervals between speciation events

  • n_int_ABC (integer) – Number of discretized time intervals in deep coalescent