metacast.infection_seeding
- 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
Makes multinomial draws selecting an infectious hosts branch and then state. |
- class metacast.infection_seeding._InfectionBranch(name, outflows)
- calculate_weighting(parameters)
Calculate normalised weighting for each state.
- Parameters:
parameters (dict {str: Number}) – Dictionary of parameter values.
- Returns:
noramlised_weightings – Dictionary normalised weighting for each state.
- Return type:
dict {str: float}
- seed_infections(n, parameters, rng=None)
Make multinomial draw to select infectious stages of this branch to seed infection into.
- Parameters:
n (int) – Number of infections to seed.
parameters (dict {str: Number}) – Dictionary of parameter values.
rng (numpy random number generator, optional.) – Random number generator to use.
- Returns:
draw_dict – Keys are states values are number of infections in state.
- Return type:
dict {str: int}
- class metacast.infection_seeding.MultinomialSeeder(branch_info)
Makes multinomial draws selecting an infectious hosts branch and then state.
- Parameters:
branch_info (nested dict) –
- 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).
- branches
Infection branches that a host can be placed upon.
- Type:
dict {str: InfectionBranch}
- parameters
Parameters (outflows) given in branch_info.
- Type:
set of strings
- seed_infections(n, branch_probability, parameters)
Draw selection of states to place infected hosts.
- set_seed(seed)
Sets random number generator seed.
- Parameters:
seed (int (>0)) –
- _seed_branches(n, branch_probability)
- seed_infections(n, branch_probability, parameters)
Draw selection of states to place infected hosts.
- Parameters:
n (int) – Number of infections to seed.
branch_probability (dict {string, float}) – Probability of being on each infection branch.
parameters (dict {str: Number}) – Dictionary of parameter values.
- Returns:
infections_draw – Keys are infected states values are number of hosts in state.
- Return type:
dict {str: int}