get_tab module

itrails.get_tab.get_ABC_precomp(dct, omegas, idx_lst)[source]

This function calculates the joint probabilities for the three-sequence CTMC.

Parameters:

  • dct (dict of matrices) – Matrix exponentials per interval

  • omegas (list of lists) – Sets of states for each matrix multiplication

  • idx_lst (list) – List of keys defining which entries of dct to use

itrails.get_tab.get_AB_precomp(dct, omegas)[source]

This function calculates the joint probabilities for the two-sequence CTMC.

Parameters:

  • dct (dict of matrices) – Matrix exponentials per interval

  • omegas (list of lists) – Sets of states for each matrix multiplication

itrails.get_tab.get_tab_AB(state_space_AB, trans_mat_AB, cut_AB, pi_AB)[source]

This functions returns a table with joint probabilities of the end probabilities per state after running a two-sequence CTMC segregated by the fate of each pair of sites.

Parameters:

  • state_space_AB (list of lists of tuples) – States of the whole state space two-sequence CTMC

  • trans_mat_AB (numeric numpy matrix) – Transition rate matrix of the two-sequence CTMC

  • cut_AB (list of floats) – Ordered cutpoints of the two-sequence CTMC

  • pi_AB (list of floats) – Starting probabilities after merging two one-sequence CTMCs.

itrails.get_tab.get_tab_ABC(state_space_ABC, trans_mat_ABC, cut_ABC, pi_ABC, names_tab_AB, n_int_AB, tmp_path)[source]

This functions returns a table with joint probabilities of the states of the HMM after running a three-sequence CTMC

Parameters:

  • state_space_ABC (list of lists of tuples) – States of the whole state space of the three-sequence CTMC

  • trans_mat_ABC (numeric numpy matrix) – Transition rate matrix of the three-sequence CTMC

  • cut_ABC (list of floats) – Ordered cutpoints of the three-sequence CTMC

  • pi_ABC (list of floats) – Starting probabilities after merging a one-sequence and a two-sequence CTMCs.

  • names_tab_AB (list of tuples) – List of fates for the starting probabilities, as outputted by get_tab_AB().

  • n_int_AB (integer) – Number of intervals in the two-sequence CTMC

itrails.get_tab.pool_AB(L, r, R)[source]
itrails.get_tab.pool_ABC(l, L, r, R)[source]
itrails.get_tab.precomp(trans_mat, times)[source]

This function precomputes the matrix exponentials given a transition rate matrix and the interval times.

Parameters:

  • trans_mat (numpy array) – The transition rate matrix of a CTMC

  • times (list) – Interval times