:py:mod:`metacast.infection_seeding`
====================================

.. py:module:: metacast.infection_seeding

.. autoapi-nested-parse::

   Creation:
       Author: Martin Grunnill
       Date: 2022/09/13
   Description: Classes for Multnomial random draw seeding of infections.

   Classes
   -------
   MultnomialSeeder
       Makes multinomial draws selecting an infectious hosts branch and then state.




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

Classes
~~~~~~~

.. autoapisummary::

   metacast.infection_seeding._InfectionBranch
   metacast.infection_seeding.MultinomialSeeder




.. py:class:: _InfectionBranch(name, outflows)


   .. py:method:: calculate_weighting(parameters)

      Calculate normalised weighting for each state.

      :param parameters: Dictionary of parameter values.
      :type parameters: dict {str: Number}

      :returns: **noramlised_weightings** -- Dictionary normalised weighting for each state.
      :rtype: dict {str: float}


   .. py:method:: seed_infections(n, parameters, rng=None)

      Make multinomial draw to select infectious stages of this branch to seed infection into.

      :param n: Number of infections to seed.
      :type n: int
      :param parameters: Dictionary of parameter values.
      :type parameters: dict {str: Number}
      :param rng: Random number generator to use.
      :type rng: numpy random number generator, optional.

      :returns: **draw_dict** -- Keys are states values are number of infections in state.
      :rtype: dict {str: int}



.. py:class:: MultinomialSeeder(branch_info)


   Makes multinomial draws selecting an infectious hosts branch and then state.

   :param branch_info:
                       First level keys are branches (str).
                           Second level keys are states (str or ints) and values are the names of parameters controlling outflows for
                           those states (str).
   :type branch_info: nested dict

   .. attribute:: branches

      Infection branches that a host can be placed upon.

      :type: dict {str: InfectionBranch}

   .. attribute:: parameters

      Parameters (outflows) given in branch_info.

      :type: set of strings

   .. method:: seed_infections(n, branch_probability, parameters)

      Draw selection of states to place infected hosts.

   .. py:method:: set_seed(seed)

      Sets random number generator seed.

      :param seed:
      :type seed: int (>0)


   .. py:method:: _seed_branches(n, branch_probability)


   .. py:method:: seed_infections(n, branch_probability, parameters)

      Draw selection of states to place infected hosts.

      :param n: Number of infections to seed.
      :type n: int
      :param branch_probability: Probability of being on each infection branch.
      :type branch_probability: dict {string, float}
      :param parameters: Dictionary of parameter values.
      :type parameters: dict {str: Number}

      :returns: **infections_draw** -- Keys are infected states values are number of hosts in state.
      :rtype: dict {str: int}