phylovelo.gillespie_variable_paras
==================================

.. py:module:: phylovelo.gillespie_variable_paras


Classes
-------

.. autoapisummary::

   phylovelo.gillespie_variable_paras.Cell
   phylovelo.gillespie_variable_paras.Reaction
   phylovelo.gillespie_variable_paras.Gillespie


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

.. py:class:: Cell(Ngene: int = None, state: int = 0, gen: int = None, cid: int = None, parent: int = None, tb: float = None, td: float = None)

   Cell class

   Args:
       Ngene: 
           Gene number
       state: 
           Cell type
       gen: 
           Cell generation
       cid: 
           Cell id
       parent: 
           Cell's parent
       tb: 
           Birth time
       td: 
           Death time


   .. py:attribute:: state
      :value: 0



   .. py:attribute:: parent
      :value: None



   .. py:attribute:: cid
      :value: None



   .. py:attribute:: gen
      :value: None



   .. py:attribute:: tb
      :value: None



   .. py:attribute:: td
      :value: None



.. py:class:: Reaction(rate: callable = None, num_lefts: list = None, num_rights: list = None, index: int = None)

   Cell division/differentiation type

   Args:
       rate:
           reaction rate function
       num_lefts:
           Cell numbers before reaction
       num_right:
           Cell numbers after reaction
       index:
           Reaction index


   .. py:attribute:: rate
      :value: None



   .. py:attribute:: num_lefts


   .. py:attribute:: num_rights


   .. py:attribute:: num_diff


   .. py:attribute:: index
      :value: None



   .. py:method:: combine(n, s)


   .. py:method:: propensity(n, t)


.. py:class:: Gillespie(num_elements: int, inits: list = None, max_cell_num: int = 20000)

   Gillespie simulation

   Args:
       num_elements: 
           Cell type number
       inits: 
           Initial cell number
       max_cell_num: 
           Maximum cell number


   .. py:attribute:: num_elements


   .. py:attribute:: reactions
      :value: []



   .. py:attribute:: anc_cells
      :value: []



   .. py:attribute:: curr_cells


   .. py:attribute:: generation_time
      :value: [0]



   .. py:attribute:: max_cell_num
      :value: 20000



   .. py:method:: add_reaction(rate: callable = None, num_lefts: list = None, num_rights: list = None, index: int = None)

      Add reactions to simulation

      Args:
          rate:
              reaction rate function
          num_lefts:
              Cell numbers before reaction
          num_right:
              Cell numbers after reaction
          index:
              Reaction index



   .. py:method:: evolute(steps: int)

      Run simulation

      Args:
          steps:
              How many steps to evolute before step