hapsburg.transitions
====================

.. py:module:: hapsburg.transitions

.. autoapi-nested-parse::

   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
-------

.. autoapisummary::

   hapsburg.transitions.Transitions
   hapsburg.transitions.Model_Transitions


Functions
---------

.. autoapisummary::

   hapsburg.transitions.load_transition_model


Module Contents
---------------

.. py:class:: Transitions(n_ref=20, r_map=[])

   Bases: :py:obj:`object`


   Class for transition probabilities.
   Has methods to return them


   .. py:attribute:: n_ref
      :value: 0



   .. py:attribute:: trans_mat
      :value: []



   .. py:attribute:: r_map
      :value: []



   .. py:method:: give_transitions()
      :abstractmethod:


      Return Transition Matrix



   .. py:method:: calc_transitions(n=0)
      :abstractmethod:


      Return Transition Matrix



   .. py:method:: set_params(**kwargs)

      Set the Values.



.. py:class:: Model_Transitions(n_ref=20, r_map=[])

   Bases: :py:obj:`Transitions`


   Implements the Model Transitions


   .. py:attribute:: roh_in
      :value: 0.0005



   .. py:attribute:: roh_out
      :value: 0.001



   .. py:attribute:: roh_jump
      :value: 0.02



   .. py:method:: calc_transitions(n=0, rate=True, submat33=True)

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



   .. py:method:: give_transitions()

      Give the transition_matrix



.. py:function:: load_transition_model(t_model='model', n_ref=20)

   Load the Transition Model