def test_pulsed_infections_network_poisson(make_test_sim):
''' Test a poisson sampled number of infections'''
pars, BU_pop = make_test_sim
# Turn off infections from person-to-person
pars['beta'] = 0
# Infect 10 people.
num_days = (bu.make_dt(pars['end_day']) -
bu.make_dt(pars['start_day'])).days
days = (num_days + 1) * [0]
# All infections on the first day.
days[0] = 1
NUM_INFECTIONS = 10
interv = bv.pulsed_infections_network(BU_pop['contacts'],
days,
layer_name='household',
pulse_sampling='poisson',
pulse_count=NUM_INFECTIONS)
sim = cv.Sim(pars=pars,
popfile=BU_pop,
verbose=False,
load_pop=True,
interventions=[interv],
analyzers=[])
# Update the sim with our extra categories
bu.update_sim_people(sim, BU_pop)
# Fix the random seed
cv.utils.set_seed(987654321)
# run it
sim.run()
# Check that the correct number of infections on day 0 were created
assert sim.results['new_infections'].values[0] == 9
# and none on day 1
assert sim.results['new_infections'].values[1] == 0
def test_gen_periodic_testing_interventions_real(make_test_sim):
# Generate tests for every 3.5 days and every 7 days. Run the sim
# for a week. Check that the sum of sim.results['new_tests'] is
# equal to the number of people in the sim. beta is set to zero
# to prevent any infections/symptomatic attestation going on and
# triggering more tests.
pars, BU_pop = make_test_sim
# Turn off infections from person-to-person
pars['beta'] = 0
# Set the dates. One week plus a day so we get a week of testing.
pars['start_day'] = '2020-01-01'
pars['end_day'] = '2020-01-08'
num_days = (bu.make_dt(pars['end_day']) -
bu.make_dt(pars['start_day'])).days
intervs = bu.gen_periodic_testing_interventions_real(
BU_pop, num_days, start_date=pars['start_day'])
sim = cv.Sim(pars=pars,
popfile=BU_pop,
verbose=False,
load_pop=True,
interventions=intervs,
analyzers=[])
# Update the sim with our extra categories
bu.update_sim_people(sim, BU_pop)
# Fix the random seed
cv.utils.set_seed(987654321)
# run it
sim.run()
# Total number of tests
assert int(sum(sim.results['new_tests'])) == 10818
# each day
assert list(sim.results['new_tests'])[0:-1] == [
1683.0, 1697.0, 1747.0, 1119.0, 1128.0, 1697.0, 1747.0
]
verbose = False # keep the simulations quiet
if n_runs == 1:
verbose = True #unles there's just 1.
#%% Create the list of daily snapshot objects
analyzers = bu.get_BU_snapshots(num_days)
#%%
sim = cv.Sim(pars=pars,
popfile=BU_pop,
verbose=verbose,
load_pop=True,
interventions=interventions,
analyzers=analyzers)
# Update the sim with our extra categories
bu.update_sim_people(sim, BU_pop)
#%%
sims_complete = bu.parallel_run_sims(sim,
n_runs=n_runs,
n_cores=bu.get_n_cores())
msim = cv.MultiSim(sims_complete)
msim.reduce()
print("Creating dataframes")
#%% Get the snapshots dataframe
snapshots_df = bu.snapshots_to_df(sims_complete)
#%%
infection_df = bu.infection_count_to_df(sims_complete)