covasim.population module

Defines functions for making the population.

covasim.population.make_people(sim, save_pop=False, popfile=None, die=True, reset=False, verbose=None, **kwargs)

Make the actual people for the simulation. Usually called via sim.initialize(), not directly by the user.

Parameters

  • sim (Sim) – the simulation object

  • save_pop (bool) – whether to save the population to disk

  • popfile (bool) – if so, the filename to save to

  • die (bool) – whether or not to fail if synthetic populations are requested but not available

  • reset (bool) – whether to force population creation even if self.popdict/self.people exists

  • verbose (bool) – level of detail to print

  • kwargs (dict) – passed to make_randpop() or make_synthpop()

Returns

people

Return type

people (People)

covasim.population.make_randpop(sim, use_age_data=True, use_household_data=True, sex_ratio=0.5, microstructure=False)

Make a random population, with contacts.

This function returns a “popdict” dictionary, which has the following (required) keys:

  • uid: an array of (usually consecutive) integers of length N, uniquely identifying each agent

  • age: an array of floats of length N, the age in years of each agent

  • sex: an array of integers of length N (not currently used, so does not have to be binary)

  • contacts: list of length N listing the contacts; see make_random_contacts() for details

  • layer_keys: a list of strings representing the different contact layers in the population; see make_random_contacts() for details

Parameters

  • sim (Sim) – the simulation object

  • use_age_data (bool) – whether to use location-specific age data

  • use_household_data (bool) – whether to use location-specific household size data

  • sex_ratio (float) – proportion of the population that is male (not currently used)

  • microstructure (bool) – whether or not to use the microstructuring algorithm to group contacts

Returns

a dictionary representing the population, with the following keys for a population of N agents with M contacts between them:

Return type

popdict (dict)

covasim.population.make_random_contacts(pop_size, contacts, overshoot=1.2, dispersion=None)

Make random static contacts.

Parameters

  • pop_size (int) – number of agents to create contacts between (N)

  • contacts (dict) – a dictionary with one entry per layer describing the average number of contacts per person for that layer

  • overshoot (float) – to avoid needing to take multiple Poisson draws

  • dispersion (float) – if not None, use a negative binomial distribution with this dispersion parameter instead of Poisson to make the contacts

Returns

a list of length N, where each entry is a dictionary by layer, and each dictionary entry is the UIDs of the agent’s contacts layer_keys (list): a list of layer keys, which is the same as the keys of the input “contacts” dictionary

Return type

contacts_list (list)

covasim.population.make_microstructured_contacts(pop_size, contacts)

Create microstructured contacts – i.e. for households

covasim.population.make_hybrid_contacts(pop_size, ages, contacts, school_ages=None, work_ages=None)

Create “hybrid” contacts – microstructured contacts for households and random contacts for schools and workplaces, both of which have extremely basic age structure. A combination of both make_random_contacts() and make_microstructured_contacts().

covasim.population.make_synthpop(sim, generate=True, layer_mapping=None, **kwargs)

Make a population using SynthPops, including contacts. Usually called automatically, but can also be called manually.

Parameters

  • sim (Sim) – a Covasim simulation object

  • generate (bool) – whether or not to generate a new population (otherwise, tries to load a pre-generated one)

  • layer_mapping (dict) – a custom mapping from SynthPops layers to Covasim layers

  • kwars (dict) – passed to sp.make_population()

Example:

sim = cv.Sim(pop_type='synthpops')
sim.popdict = cv.make_synthpop(sim)
sim.run()