lineage.Viterbi
===============

.. py:module:: lineage.Viterbi

.. autoapi-nested-parse::

   This file contains the methods for the Viterbi algorithm implemented in an upward recursion.



Functions
---------

.. autoapisummary::

   lineage.Viterbi.get_deltas
   lineage.Viterbi.Viterbi


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

.. py:function:: get_deltas(X, E, T)

   Delta matrix and base case at the leaves.
   Each element in this N by K matrix is the probability for the leaves :math:`P(x_n = x | z_n = k)`.

   Then calculates delta values for non-leaf cells by filling out the delta matrix.

   :param X: list of lineage trees
   :param E: list of emission distributions
   :param T: transition probability matrix
   :return: deltas and state pointers for each lineage


.. py:function:: Viterbi(tHMMobj)

   Runs the Viterbi algorithm and returns a list of arrays containing the optimal state of each cell.
   This function returns the most likely sequence of states for each lineage.

   :param tHMMobj: a class object with properties of the lineages of cells
   :return: assigned states to each cell in all lineages