def test_option_susceptibility():
args = parse_args(
["--popsize", "A=500", "B=300", "--susceptibility", "A=0.8"])
params = Params(args)
assert sorted(list(params.groups.keys())) == ["A", "B"]
assert params.susceptibility_multiplier_A == 0.8
with pytest.raises(AttributeError):
params.susceptibility_multiplier_B
# group does not exist
with pytest.raises(ValueError):
args = parse_args(
["--popsize", "A=500", "B=300", "--susceptibility", "C=0.8"])
params = Params(args)
# not float
with pytest.raises(ValueError):
args = parse_args(
["--popsize", "A=500", "B=300", "--susceptibility", "A=1f"])
params = Params(args)
args = parse_args(
["--popsize", "A=500", "B=300", "--susceptibility", "0.8"])
params = Params(args)
def summarize_model(self, simu_args, args):
print(f"\nPlugin {self}:")
model = Model(Params(simu_args))
for asym_carriers in (0, 1, None):
if asym_carriers is not None:
model.params.set("prop_asym_carriers", "loc", asym_carriers)
model.params.set("prop_asym_carriers", "scale", 0)
else:
model = Model(Params(simu_args))
# average test sensitivity
sensitivities7 = []
sensitivities20 = []
with open(os.devnull, "w") as logger:
logger.id = 1
for i in range(10000):
model.draw_prop_asym_carriers()
ind = Individual(id="0",
susceptibility=1,
model=model,
logger=logger)
ind.infect(0, by=None, leadtime=0)
for i in range(20):
test_lod = (args.sensitivity[1]
if len(args.sensitivity) == 2 else 0)
lod_sensitivity = ind.test_sensitivity(i, test_lod)
if lod_sensitivity == 0:
continue
#
sensitivity = lod_sensitivity * args.sensitivity[0]
if i <= 7:
sensitivities7.append(sensitivity)
else:
sensitivities20.append(sensitivity)
print(
f"\nTest sensitivity (for {model.params.prop_asym_carriers*100:.1f}% asymptomatic carriers)"
)
print(
f" <= 7 days: {pd.Series(sensitivities7).mean() * 100:.1f}%"
)
print(
f" > 7 days: {pd.Series(sensitivities20).mean() * 100:.1f}%"
)
print(
f" all: {pd.Series(sensitivities7 + sensitivities20).mean() * 100:.1f}%"
)
def test_option_popsize():
args = parse_args(["--popsize", "500"])
params = Params(args)
assert list(params.groups.keys()) == [""]
args = parse_args(["--popsize", "A=500", "B=300"])
params = Params(args)
assert sorted(list(params.groups.keys())) == ["A", "B"]
args = parse_args(["--popsize", "A=500", "B=300"])
params = Params(args)
assert sorted(list(params.groups.keys())) == ["A", "B"]
with pytest.raises(ValueError):
args = parse_args(["--popsize", "500", "300"])
params = Params(args)
with pytest.raises(ValueError):
args = parse_args(["--popsize", "50A"])
params = Params(args)
with pytest.raises(ValueError):
args = parse_args(["--popsize", "all=100"])
params = Params(args)
with pytest.raises(ValueError):
args = parse_args(["--popsize", "500", "A=300", "A=200"])
params = Params(args)
def test_option_prop_asym_carriers():
args = parse_args(["--prop-asym-carriers", "0.1"])
params = Params(args)
assert params.prop_asym_carriers_loc == 0.1
assert params.prop_asym_carriers_scale == 0.0
args = parse_args(["--prop-asym-carriers", "0.1", "0.3"])
params = Params(args)
assert params.prop_asym_carriers_loc == 0.2
# not a float number
with pytest.raises(ValueError):
args = parse_args(
["--popsize", "A=10", "B=10", "--prop-asym-carriers", "1.2f"])
params = Params(args)
# not incremental
with pytest.raises(ValueError):
args = parse_args([
"--popsize", "A=10", "B=10", "--prop-asym-carriers", "1.5", "0.5"
])
params = Params(args)
# more numbers
with pytest.raises(ValueError):
args = parse_args([
"--popsize", "A=10", "B=10", "--prop-asym-carriers", "1.5", "2.5",
"3.5"
])
params = Params(args)
with pytest.raises(ValueError):
args = parse_args(
["--popsize", "A=10", "B=10", "--prop-asym-carriers", "C=1.2"])
params = Params(args)
with pytest.raises(ValueError):
args = parse_args(
["--popsize", "A=10", "B=10", "--prop-asym-carriers", "A=-1.2"])
params = Params(args)
with pytest.raises(ValueError):
args = parse_args(
["--popsize", "A=10", "B=10", "--prop-asym-carriers", "A=1.2f"])
params = Params(args)
args = parse_args(
["--popsize", "A=10", "B=10", "--prop-asym-carriers", "A=1.2"])
params = Params(args)
assert params.prop_asym_carriers_multiplier_A == 1.2
def test_option_infectors():
args = parse_args(["--infectors", "10"])
params = Params(args)
args = parse_args(
["--popsize", "A=10", "B=10", "--infectors", "A_1", "B_2"])
params = Params(args)
with pytest.raises(ValueError):
args = parse_args(["--popsize", "A=10", "B=10", "--infectors", "1"])
params = Params(args)
with pytest.raises(ValueError):
args = parse_args(
["--popsize", "A=10", "B=10", "--infectors", "C_1", "C_2"])
params = Params(args)
with pytest.raises(ValueError):
args = parse_args(["--popsize", "A=10", "B=10", "--infectors", "A_10"])
params = Params(args)
def test_option_symptomatic_r0():
args = parse_args(["--symptomatic-r0", "1.0"])
params = Params(args)
assert params.symptomatic_r0_loc == 1.0
assert params.symptomatic_r0_scale == 0
args = parse_args(["--symptomatic-r0", "1.2", "2.0"])
params = Params(args)
assert params.symptomatic_r0_loc == (1.2 + 2.0) / 2
args = parse_args(
["--popsize", "A=500", "B=300", "--symptomatic-r0", "1.5", "A=0.8"])
params = Params(args)
assert sorted(list(params.groups.keys())) == ["A", "B"]
assert params.symptomatic_r0_loc == 1.5
assert params.symptomatic_r0_scale == 0
assert params.symptomatic_r0_multiplier_A == 0.8
# not float number
with pytest.raises(ValueError):
args = parse_args(["--symptomatic-r0", "1.0f"])
params = Params(args)
with pytest.raises(ValueError):
args = parse_args(["--symptomatic-r0", "0.8a", "1.0"])
params = Params(args)
with pytest.raises(ValueError):
args = parse_args(["--symptomatic-r0", "0.8", "1.0f"])
params = Params(args)
with pytest.raises(ValueError):
args = parse_args(["--popsize", "A=200", "--symptomatic-r0", "A=8b"])
params = Params(args)
# more numbers
with pytest.raises(ValueError):
args = parse_args(["--symptomatic-r0", "0.8", "1.0", "2.0"])
params = Params(args)
def test_option_inclubation_period():
with pytest.raises(ValueError):
args = parse_args(["--incubation-period", "1.0"])
params = Params(args)
with pytest.raises(ValueError):
args = parse_args(["--incubation-period", "1.0", "2.0"])
params = Params(args)
with pytest.raises(ValueError):
args = parse_args(["--incubation-period", "uniform", "1.0", "2.0"])
params = Params(args)
with pytest.raises(ValueError):
args = parse_args(
["--popsize", "A=100", "B=200", "--incubation-period", "C=0.8"])
params = Params(args)
args = parse_args(["--incubation-period", "normal", "1.2", "2.0"])
params = Params(args)
assert params.incubation_period_loc == 1.2
assert params.incubation_period_scale == 2.0
args = parse_args(["--incubation-period", "lognormal", "1.", "2.5"])
params = Params(args)
assert params.incubation_period_mean == 1.0
assert params.incubation_period_sigma == 2.5
args = parse_args(
["--popsize", "A=500", "B=300", "--incubation-period", "A=0.8"])
params = Params(args)
assert sorted(list(params.groups.keys())) == ["A", "B"]
assert params.incubation_period_multiplier_A == 0.8
args = parse_args([
"--popsize",
"A=500",
"B=300",
"--incubation-period",
"normal",
"5",
"2",
"B=0.95",
"A=1.13",
])
params = Params(args)
assert sorted(list(params.groups.keys())) == ["A", "B"]
assert params.incubation_period_loc == 5.0
assert params.incubation_period_scale == 2.0
assert params.incubation_period_multiplier_A == 1.13
assert params.incubation_period_multiplier_B == 0.95
with pytest.raises(ValueError):
args = parse_args([
"--popsize",
"A=500",
"B=300",
"--incubation-period",
"normal",
"5",
"2.3p",
])
params = Params(args)
with pytest.raises(ValueError):
args = parse_args([
"--popsize",
"A=500",
"B=300",
"--incubation-period",
"normal",
"5",
"2.3p",
"A=1.4p",
])
params = Params(args)
# negative multiplier
with pytest.raises(ValueError):
args = parse_args(
["--popsize", "A=500", "B=300", "--incubation-period", "A=-1"])
params = Params(args)
# non-float multiplier
with pytest.raises(ValueError):
args = parse_args(
["--popsize", "A=500", "B=300", "--incubation-period", "A=1f"])
params = Params(args)
def default_model():
return Model(Params())
def params():
return Params()