def bypass():
do_plot = True # Whether to plot results
n_seeds = 6 # Number of seeds to run each simulation with
rand_seed = 1 # Overwrite the default random seed
bypass_popfile = 'trans_r0_medium.ppl'
pop_size = int(100e3)
entry = {
"index": 376.0,
"mismatch": 0.03221581045452142,
"pars": {
"pop_infected": 0,
"change_beta": 0.5313884845187986,
"symp_prob": 0.08250498122080606
}
}
params = sc.dcp(entry['pars'])
if rand_seed is None:
params['rand_seed'] = int(entry['index'])
else:
params['rand_seed'] = rand_seed
# Ensure the population file exists
if not os.path.exists(bypass_popfile):
print(f'Population file {bypass_popfile} not found, recreating...')
cvsch.make_population(pop_size=pop_size,
rand_seed=params['rand_seed'],
max_pop_seeds=5,
popfile=bypass_popfile,
do_save=True)
scen = generate_scenarios()['as_normal']
# Create the sim
people = sc.loadobj(bypass_popfile)
base_sim = cs.create_sim(params,
pop_size=pop_size,
load_pop=False,
people=people,
verbose=0.1)
# Run the sims
sims = []
for seed in range(n_seeds):
sim = sc.dcp(base_sim)
sim.set_seed(seed=sim['rand_seed'] + seed)
sim.label = f'Sim {seed}'
sim['interventions'] += [cvsch.schools_manager(scen), seed_schools()]
sim['beta_layer'] = dict(
h=0.0, s=0.0, w=0.0, c=0.0, l=0.0
) # Turn off transmission in other layers, looking for in-school R0
sims.append(sim)
msim = cv.MultiSim(sims)
msim.run(keep_people=True)
return msim
def longway():
pop_size = 2.25e5
calibfile = os.path.join(
folder,
'pars_cases_begin=75_cases_end=75_re=1.0_prevalence=0.002_yield=0.024_tests=225_pop_size=225000.json'
)
par_list = sc.loadjson(calibfile)[par_inds[0]:par_inds[1]]
scen = generate_scenarios()['as_normal']
for stype, cfg in scen.items():
if cfg:
cfg['start_day'] = '2020-09-07' # Move school start earlier
# Configure and run the sims
sims = []
for eidx, entry in enumerate(par_list):
par = sc.dcp(entry['pars'])
par['rand_seed'] = int(entry['index'])
# Clunky, but check that the population exists
pop_seed = par['rand_seed'] % 5
popfile = os.path.join(
folder, 'inputs',
f'kc_synthpops_clustered_{int(pop_size)}_withstaff_seed') + str(
pop_seed) + '.ppl'
if not os.path.exists(popfile):
print(f'Population file {popfile} not found, recreating...')
cvsch.make_population(pop_size=pop_size,
rand_seed=par['rand_seed'],
max_pop_seeds=5,
popfile=popfile,
do_save=True)
par['pop_infected'] = 0 # Do NOT seed infections
par['beta_layer'] = dict(
h=0.0, s=0.0, w=0.0, c=0.0, l=0.0
) # Turn off transmission in other layers, looking for in-school R0
sim = cs.create_sim(par, pop_size=pop_size, folder=folder)
delay = sim.day('2020-09-16') # Pick a Monday
sim['interventions'] += [
cvsch.schools_manager(scen),
seed_schools(delay=delay, n_infections=1, choose_students=False)
]
sims.append(sim)
msim = cv.MultiSim(sims)
msim.run(keep_people=True)
return msim
# Modify scen
for stype, spec in scen.items():
if spec is not None:
spec['screen_prob'] = 0
return scen
def no_tracing(sim, scen, test):
# Modify scen
for stype, spec in scen.items():
if spec is not None:
spec['trace_prob'] = 0
return scen
if __name__ == '__main__':
scenarios = t_s.generate_scenarios()
#scenarios = {k:v for k,v in scenarios.items() if k in ['with_countermeasures', 'all_hybrid', 'k5', 'all_remote']}
scenarios = {k:v for k,v in scenarios.items() if k in ['with_countermeasures']}
testing = t_s.generate_testing()
#testing = {k:v for k,v in testing.items() if k in ['None', 'PCR every 2w', 'Antigen every 1w teach&staff, PCR f/u', 'Antigen every 2w, PCR f/u']}
testing = {k:v for k,v in testing.items() if k in ['None', 'Antigen every 2w, PCR f/u']}
sensitivity = {
# Baseline
'baseline': [baseline],
# For K-5 in particular, masks could be challenging - what if we remove the 25% NPI boost?
# --> Change beta in the scenario
'NPI': [baseline, no_NPI_reduction],
other_edges = edges_this_school.loc[
(~edges_this_school['p1_student']) |
(~edges_this_school['p2_student'])]
rewired_edges_this_school = pd.concat(
[rewired_student_to_student_edges, other_edges])
school_contacts.append(rewired_edges_this_school)
all_school_contacts = pd.concat(school_contacts)
sim.people.contacts['s'] = cv.Layer().from_df(all_school_contacts)
sm = cvsch.schools_manager(scen)
sim['interventions'] += [sm]
if __name__ == '__main__':
scenarios = generate_scenarios()
#scenarios = {k:v for k,v in scenarios.items() if k in ['with_countermeasures', 'all_hybrid', 'k5', 'all_remote']}
scenarios = {k: v for k, v in scenarios.items() if k in ['k5']}
testing = generate_testing()
testing = {
k: v
for k, v in testing.items() if k in [
'None',
'PCR every 2w',
#'Antigen every 2w, PCR f/u',
'Antigen every 2w, no f/u',
'Antigen every 1w, PCR f/u',
#'Antigen every 1w teach&staff, PCR f/u',
]
}
