synthpops.people.makepop module

Defines functions for making the population.

make_people(n=None, popdict=None, rand_seed=1, pop_type='synthpops', location=None, save_pop=False, popfile=None, die=True, verbose=None, **kwargs)

Make the actual people for the simulation. Usually called via sim.initialize(), but can be called directly by the user.

Parameters:

• n (int) – the number of people to create
• popdict (dict) – if supplied, use this population dictionary instead of generating a new one
• 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
• verbose (bool) – level of detail to print
• kwargs (dict) – passed to make_randpop() or make_synthpop()

Returns:

people

Return type:

people (People)

New in version 1.10.0.

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)

New in version 1.10.0.

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)

New in version 1.10.0.

make_microstructured_contacts(pop_size, contacts)

Create microstructured contacts – i.e. for households

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().

New in version 1.10.0.

parse_synthpop(population, layer_mapping=None, community_contacts=0)

Make a population using SynthPops, including contacts. Usually called automatically, but can also be called manually. Either a simulation object or a population must be supplied; if a population is supplied, transform it into the correct format; otherwise, create the population and then transform it.

Parameters:

• population (list) – a pre-generated SynthPops population
• layer_mapping (dict) – a custom mapping from SynthPops layers to Covasim layers
• community_contacts (int) – create this many community contacts on average

New in version 1.10.0.