def __init__(self,
npts,
symptomatic_prob=0.9,
asymptomatic_prob=0.01,
trace_prob=1.0,
test_sensitivity=1.0):
"""
Args:
self:
symptomatic_prob:
trace_prob:
Returns:
"""
super().__init__()
self.symptomatic_prob = symptomatic_prob
self.asymptomatic_prob = asymptomatic_prob
self.trace_prob = trace_prob # Probability that identified contacts get tested
self.test_sensitivity = test_sensitivity
# Instantiate the results to track
self.results['n_tested'] = cv.Result('Number tested', npts=npts)
self.results['n_diagnosed'] = cv.Result('Number diagnosed', npts=npts)
self.results['cum_tested'] = cv.Result('Cumulative number tested',
npts=npts)
self.results['cum_diagnosed'] = cv.Result(
'Cumulative number diagnosed', npts=npts)
self.scheduled_tests = set(
) # Track UIDs of people that are guaranteed to be tested at the next step
return
def finalize(self, sim, *args, **kwargs):
self.results['cum_tested'] = cv.Result(
'Cumulative number tested',
values=pl.cumsum(self.results['n_tested'].values))
self.results['cum_diagnosed'] = cv.Result(
'Cumulative number diagnosed',
values=pl.cumsum(self.results['n_diagnosed'].values))
sim.results.update(self.results)
return
def __init__(self, npts, n_tests, n_positive):
"""
Args:
npts: Number of simulation timepoints
n_tests: Number of tests per day. If this is a scalar or an array with length less than npts, it will be zero-padded
n_positive: Number of positive tests (confirmed cases) per day. If this is a scalar or an array with length less than npts, it will be zero-padded
"""
super().__init__()
self.n_tests = np.pad(sc.promotetoarray(n_tests),
(0, max(0, npts - len(n_tests))))
self.n_positive = np.pad(sc.promotetoarray(n_positive),
(0, max(0, npts - len(n_positive))))
self.results['n_tested'] = cv.Result('Number tested', npts=npts)
self.results['n_diagnosed'] = cv.Result('Number diagnosed', npts=npts)
def __init__(self,
npts,
daily_tests,
sympt_test=100.0,
trace_test=1.0,
sensitivity=1.0):
super().__init__()
self.daily_tests = daily_tests #: Should be a list of length matching time
self.sympt_test = sympt_test
self.trace_test = trace_test
self.sensitivity = sensitivity
self.results['n_diagnosed'] = cv.Result('Number diagnosed', npts=npts)
self.results['cum_diagnosed'] = cv.Result(
'Cumulative number diagnosed', npts=npts)
return
def test_base():
sc.heading('Testing base.py sim...')
json_path = 'base_tests.json'
sim_path = 'base_tests.sim'
# Create a small sim for later use
sim = cv.Sim(pop_size=100, verbose=verbose)
sim.run()
# Check setting invalid key
with pytest.raises(sc.KeyNotFoundError):
po = cv.ParsObj(pars={'a': 2, 'b': 3})
po.update_pars({'c': 4})
# Printing result
r = cv.Result()
print(r)
print(r.npts)
# Day and date conversion
daystr = '2020-04-04'
sim.day(daystr)
sim.day(sc.readdate(daystr))
with pytest.raises(ValueError):
sim.day('not a date')
sim.date(34)
sim.date([34, 54])
sim.date(34, 54, as_date=True)
# BaseSim methods
sim.copy()
sim.export_results(filename=json_path)
sim.export_pars(filename=json_path)
sim.shrink(in_place=False)
for keep_people in [True, False]:
sim.save(filename=sim_path, keep_people=keep_people)
cv.Sim.load(sim_path)
# Tidy up
remove_files(json_path, sim_path)
return
def test_base():
sc.heading('Testing base.py...')
json_path = 'base_tests.json'
sim_path = 'base_tests.sim'
# Create a small sim for later use
sim = cv.Sim(pop_size=100, verbose=verbose)
sim.run()
# Check setting invalid key
with pytest.raises(sc.KeyNotFoundError):
po = cv.ParsObj(pars={'a': 2, 'b': 3})
po.update_pars({'c': 4})
# Printing result
r = cv.Result()
print(r)
print(r.npts)
# Day and date conversion
daystr = '2020-04-04'
sim.day(daystr)
sim.day(sc.readdate(daystr))
with pytest.raises(ValueError):
sim.day('not a date')
sim.date(34)
sim.date([34, 54])
sim.date(34, 54, as_date=True)
# BaseSim methods
sim.copy()
sim.export_results(filename=json_path)
sim.export_pars(filename=json_path)
sim.shrink(in_place=False)
for keep_people in [True, False]:
sim.save(filename=sim_path, keep_people=keep_people)
cv.Sim.load(sim_path)
# BasePeople methods
ppl = sim.people
ppl.get(['susceptible', 'infectious'])
ppl.keys(which='all_states')
ppl.index()
ppl.resize(pop_size=200)
ppl.to_df()
ppl.to_arr()
ppl.person(50)
people = ppl.to_people()
ppl.from_people(people)
with pytest.raises(sc.KeyNotFoundError):
ppl.make_edgelist([{'invalid_key': [0, 1, 2]}])
# Contacts methods
contacts = ppl.contacts
df = contacts['a'].to_df()
ppl.remove_duplicates(df)
with pytest.raises(sc.KeyNotFoundError):
contacts['invalid_key']
contacts.values()
len(contacts)
# Transmission tree methods
ppl.transtree.make_targets()
ppl.make_detailed_transtree()
ppl.transtree.plot()
ppl.transtree.animate(animate=False)
# Tidy up
remove_files(json_path, sim_path)
return
def test_base():
sc.heading('Testing base.py...')
json_path = 'base_tests.json'
sim_path = 'base_tests.sim'
# Create a small sim for later use
sim = cv.Sim(pop_size=100, verbose=verbose)
sim.run()
# Check setting invalid key
with pytest.raises(sc.KeyNotFoundError):
po = cv.ParsObj(pars={'a':2, 'b':3})
po.update_pars({'c':4})
# Printing result
r = cv.Result()
print(r)
print(r.npts)
# Day and date conversion
daystr = '2020-04-04'
sim.day(daystr)
sim.day(sc.readdate(daystr))
with pytest.raises(ValueError):
sim.day('not a date')
sim.date(34)
sim.date([34, 54])
sim.date(34, 54, as_date=True)
# BaseSim methods
sim.copy()
sim.export_results(filename=json_path)
sim.export_pars(filename=json_path)
sim.shrink(in_place=False)
for keep_people in [True, False]:
sim.save(filename=sim_path, keep_people=keep_people)
cv.Sim.load(sim_path)
# BasePeople methods
ppl = sim.people
ppl.get(['susceptible', 'infectious'])
ppl.keys()
ppl.person_keys()
ppl.state_keys()
ppl.date_keys()
ppl.dur_keys()
ppl.indices()
ppl._resize_arrays(pop_size=200) # This only resizes the arrays, not actually create new people
ppl._resize_arrays(pop_size=100) # Change back
ppl.to_df()
ppl.to_arr()
ppl.person(50)
people = ppl.to_people()
ppl.from_people(people)
ppl.make_edgelist([{'new_key':[0,1,2]}])
ppl.brief()
# Contacts methods
contacts = ppl.contacts
df = contacts['a'].to_df()
ppl.remove_duplicates(df)
with pytest.raises(sc.KeyNotFoundError):
contacts['invalid_key']
contacts.values()
len(contacts)
print(contacts)
print(contacts['a'])
# Layer methods
hospitals_layer = cv.Layer()
contacts.add_layer(hospitals=hospitals_layer)
contacts.pop_layer('hospitals')
df = hospitals_layer.to_df()
hospitals_layer.from_df(df)
# Tidy up
remove_files(json_path, sim_path)
return