hapsburg.transitions

Class for calculating Transition Probabilities, i.e. infitesimal transition Matrices. Contains Sub-Classes, as well as factory Method. @ Author: Harald Ringbauer, 2019, All rights reserved

Classes

Transitions	Class for transition probabilities.
Model_Transitions	Implements the Model Transitions

Functions

load_transition_model([t_model, n_ref])

Load the Transition Model

Module Contents

class hapsburg.transitions.Transitions(n_ref=20, r_map=[])

Bases: object

Class for transition probabilities. Has methods to return them

n_ref = 0

trans_mat = []

r_map = []

abstractmethod give_transitions()

Return Transition Matrix

abstractmethod calc_transitions(n=0)

Return Transition Matrix

set_params(**kwargs)

Set the Values.

class hapsburg.transitions.Model_Transitions(n_ref=20, r_map=[])

Bases: Transitions

Implements the Model Transitions

roh_in = 0.0005

roh_out = 0.001

roh_jump = 0.02

calc_transitions(n=0, rate=True, submat33=True)

Return Transition Matrix to exponate. n: Nr of Reference Haplotypes submat33: Whether to only fill in

give_transitions()

Give the transition_matrix

hapsburg.transitions.load_transition_model(t_model='model', n_ref=20)

Load the Transition Model