def test_add_entry_flows_post_stratification():
"""
Ensure we can add flows after a model is stratified.
"""
model = CompartmentalModel(
times=[0, 5], compartments=["S", "I", "R"], infectious_compartments=["I"]
)
assert len(model._flows) == 0
strat = Stratification("location", ["urban", "rural"], ["S", "I", "R"])
model.stratify_with(strat)
with pytest.raises(AssertionError):
model.add_importation_flow("imports", 10, "S", expected_flow_count=1)
assert len(model._flows) == 0
model.add_importation_flow("imports", 10, "S", expected_flow_count=2)
assert len(model._flows) == 2
expected_flows = [
ImportFlow("imports", C("S", {"location": "urban"}), 10, []),
ImportFlow("imports", C("S", {"location": "rural"}), 10, []),
]
assert len(expected_flows) == len(model._flows)
assert all([a._is_equal(e) for e, a in zip(expected_flows, model._flows)])
def test_stratify_entry_flows__with_no_explicit_adjustments():
"""
Ensure entry flows are stratified correctly when no adjustments are requested.
Expect flow to be conserved, split evenly over the new strata.
"""
model = CompartmentalModel(
times=[0, 5], compartments=["S", "I", "R"], infectious_compartments=["I"]
)
model.add_importation_flow("imports", 10, "S")
expected_flows = [ImportFlow("imports", C("S"), 10)]
assert len(expected_flows) == len(model._flows)
assert all([a._is_equal(e) for e, a in zip(expected_flows, model._flows)])
strat = Stratification("location", ["urban", "rural"], ["S", "I", "R"])
model.stratify_with(strat)
expected_flows = [
ImportFlow("imports", C("S", {"location": "urban"}), 10, [Multiply(0.5)]),
ImportFlow("imports", C("S", {"location": "rural"}), 10, [Multiply(0.5)]),
]
assert len(expected_flows) == len(model._flows)
assert all([a._is_equal(e) for e, a in zip(expected_flows, model._flows)])
strat = Stratification("age", ["young", "old"], ["S", "I", "R"])
model.stratify_with(strat)
expected_flows = [
ImportFlow(
"imports",
C("S", {"location": "urban", "age": "young"}),
10,
[Multiply(0.5), Multiply(0.5)],
),
ImportFlow(
"imports",
C("S", {"location": "urban", "age": "old"}),
10,
[Multiply(0.5), Multiply(0.5)],
),
ImportFlow(
"imports",
C("S", {"location": "rural", "age": "young"}),
10,
[Multiply(0.5), Multiply(0.5)],
),
ImportFlow(
"imports",
C("S", {"location": "rural", "age": "old"}),
10,
[Multiply(0.5), Multiply(0.5)],
),
]
assert len(expected_flows) == len(model._flows)
assert all([a._is_equal(e) for e, a in zip(expected_flows, model._flows)])
def test_add_entry_flows_post_stratification__with_filter():
"""
Ensure we can add flows after a model is stratified when a strata filter is applied
"""
model = CompartmentalModel(
times=[0, 5], compartments=["S", "I", "R"], infectious_compartments=["I"]
)
assert len(model._flows) == 0
strat = Stratification("location", ["urban", "rural"], ["S", "I", "R"])
model.stratify_with(strat)
assert len(model._flows) == 0
model.add_importation_flow(
"imports", 10, "S", dest_strata={"location": "urban"}, expected_flow_count=1
)
assert len(model._flows) == 1
expected_flows = [
ImportFlow("imports", C("S", {"location": "urban"}), 10, []),
]
assert len(expected_flows) == len(model._flows)
assert all([a._is_equal(e) for e, a in zip(expected_flows, model._flows)])
def test_stratify_entry_flows__with_explicit_adjustments():
"""
Ensure entry flows are stratified correctly when adjustments are requested.
"""
model = CompartmentalModel(
times=[0, 5], compartments=["S", "I", "R"], infectious_compartments=["I"]
)
model.add_importation_flow("imports", 10, "S")
expected_flows = [ImportFlow("imports", C("S"), 10)]
assert len(expected_flows) == len(model._flows)
assert all([a._is_equal(e) for e, a in zip(expected_flows, model._flows)])
strat = Stratification("location", ["urban", "rural"], ["S", "I", "R"])
strat.add_flow_adjustments("imports", {"urban": Multiply(0.9), "rural": None})
model.stratify_with(strat)
expected_flows = [
ImportFlow(
"imports",
C("S", {"location": "urban"}),
10,
[Multiply(0.9)],
),
ImportFlow(
"imports",
C("S", {"location": "rural"}),
10,
[],
),
]
assert len(expected_flows) == len(model._flows)
assert all([a._is_equal(e) for e, a in zip(expected_flows, model._flows)])
strat = Stratification("age", ["young", "old"], ["S", "I", "R"])
strat.add_flow_adjustments("imports", {"young": Multiply(0.8), "old": Overwrite(1)})
model.stratify_with(strat)
expected_flows = [
ImportFlow(
"imports",
C("S", {"location": "urban", "age": "young"}),
10,
[Multiply(0.9), Multiply(0.8)],
),
ImportFlow(
"imports",
C("S", {"location": "urban", "age": "old"}),
10,
[Multiply(0.9), Overwrite(1)],
),
ImportFlow(
"imports",
C("S", {"location": "rural", "age": "young"}),
10,
[Multiply(0.8)],
),
ImportFlow(
"imports",
C("S", {"location": "rural", "age": "old"}),
10,
[Overwrite(1)],
),
]
assert len(expected_flows) == len(model._flows)
assert all([a._is_equal(e) for e, a in zip(expected_flows, model._flows)])