rsvsim.population module

Defines functions for making the population.

rsvsim.population.make_people(sim, popdict=None, save_pop=False, popfile=None, die=True, reset=False, verbose=None, **kwargs)[source]

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

Parameters

  • sim (Sim) – the simulation object; population parameters are taken from the sim object

  • 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

  • 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)

rsvsim.population.make_randpop(pars, use_age_data=True, use_household_data=True, microstructure='random', **kwargs)[source]

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

  • pars (dict) – the parameter dictionary or 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

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

  • kwargs (dict) – passed to contact creation method (e.g., make_hybrid_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)

rsvsim.population.make_random_contacts(pop_size, contacts, overshoot=1.2, dispersion=None)[source]

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)

rsvsim.population.make_microstructured_contacts(pop_size, contacts)[source]

Create microstructured contacts – i.e. for households

rsvsim.population.make_hybrid_contacts(pop_size, ages, contacts, school_ages=None)[source]

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

rsvsim.population.make_synthpop(sim=None, population=None, layer_mapping=None, community_contacts=None, **kwargs)[source]

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

  • sim (Sim) – a rsvsim simulation object

  • population (list) – a pre-generated SynthPops population (otherwise, create a new one)

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

  • community_contacts (int) – if a simulation is not supplied, create this many community contacts on average

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

Example:

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