def test_coalescent_likelihood_smoke(duration, forecast, options, algo):
population = 100
incubation_time = 2.0
recovery_time = 7.0
# Generate data.
model = SuperspreadingSEIRModel(
population, incubation_time, recovery_time, [None] * duration)
for attempt in range(100):
data = model.generate({"R0": 1.5, "rho": 0.5, "k": 1.0})["obs"]
if data.sum():
break
assert data.sum() > 0, "failed to generate positive data"
leaf_times = torch.rand(5).pow(0.5) * duration
coal_times = dist.CoalescentTimes(leaf_times).sample()
coal_times = coal_times[..., torch.randperm(coal_times.size(-1))]
# Infer.
model = SuperspreadingSEIRModel(
population, incubation_time, recovery_time, data,
leaf_times=leaf_times, coal_times=coal_times)
num_samples = 5
if algo == "mcmc":
model.fit_mcmc(warmup_steps=2, num_samples=num_samples, max_tree_depth=2,
**options)
else:
model.fit_svi(num_steps=2, num_samples=num_samples, **options)
# Predict and forecast.
samples = model.predict(forecast=forecast)
assert samples["S"].shape == (num_samples, duration + forecast)
assert samples["E"].shape == (num_samples, duration + forecast)
assert samples["I"].shape == (num_samples, duration + forecast)
def test_superspreading_seir_smoke(duration, forecast, options):
population = 100
incubation_time = 2.0
recovery_time = 7.0
# Generate data.
model = SuperspreadingSEIRModel(
population, incubation_time, recovery_time, [None] * duration
)
assert model.full_mass == [("R0", "k", "rho")]
for attempt in range(100):
data = model.generate({"R0": 1.5, "rho": 0.5, "k": 1.0})["obs"]
if data.sum():
break
assert data.sum() > 0, "failed to generate positive data"
# Infer.
model = SuperspreadingSEIRModel(population, incubation_time, recovery_time, data)
num_samples = 5
model.fit_mcmc(warmup_steps=2, num_samples=num_samples, max_tree_depth=2, **options)
# Predict and forecast.
samples = model.predict(forecast=forecast)
assert samples["S"].shape == (num_samples, duration + forecast)
assert samples["E"].shape == (num_samples, duration + forecast)
assert samples["I"].shape == (num_samples, duration + forecast)
def Model(args, data):
"""Dispatch between different model classes."""
if args.heterogeneous:
assert args.incubation_time == 0
assert args.overdispersion == 0
return HeterogeneousSIRModel(args.population, args.recovery_time, data)
elif args.incubation_time > 0:
assert args.incubation_time > 1
if args.concentration < math.inf:
return SuperspreadingSEIRModel(args.population,
args.incubation_time,
args.recovery_time, data)
elif args.overdispersion > 0:
return OverdispersedSEIRModel(args.population,
args.incubation_time,
args.recovery_time, data)
else:
return SimpleSEIRModel(args.population, args.incubation_time,
args.recovery_time, data)
else:
if args.concentration < math.inf:
return SuperspreadingSIRModel(args.population, args.recovery_time,
data)
elif args.overdispersion > 0:
return OverdispersedSIRModel(args.population, args.recovery_time,
data)
else:
return SimpleSIRModel(args.population, args.recovery_time, data)