def test_beta_coalescent_parameters(self):
N = 1000
dbl_max = sys.float_info.max
for alpha in [1.01, 1.5, 1.99]:
model = msprime.BetaCoalescent(N, alpha)
self.assertEqual(model.population_size, N)
self.assertEqual(model.alpha, alpha)
self.assertEqual(model.truncation_point, dbl_max)
d = model.get_ll_representation()
self.assertEqual(
d, {
"name": "beta",
"population_size": N,
"alpha": alpha,
"truncation_point": dbl_max
})
alpha = 1.5
for truncation_point in [0, 3, 1e6]:
model = msprime.BetaCoalescent(N, alpha, truncation_point)
self.assertEqual(model.population_size, N)
self.assertEqual(model.alpha, alpha)
self.assertEqual(model.truncation_point, truncation_point)
d = model.get_ll_representation()
self.assertEqual(
d, {
"name": "beta",
"population_size": N,
"alpha": alpha,
"truncation_point": truncation_point
})
def test_beta_coalescent_parameters(self):
for alpha in [1.01, 1.5, 1.99]:
model = msprime.BetaCoalescent(alpha)
self.assertEqual(model.alpha, alpha)
self.assertEqual(model.truncation_point, 1)
d = model.get_ll_representation()
self.assertEqual(
d,
{
"name": "beta",
"alpha": alpha,
"truncation_point": 1
},
)
alpha = 1.5
for truncation_point in [0.01, 0.5, 1]:
model = msprime.BetaCoalescent(alpha, truncation_point)
self.assertEqual(model.alpha, alpha)
self.assertEqual(model.truncation_point, truncation_point)
d = model.get_ll_representation()
self.assertEqual(
d,
{
"name": "beta",
"alpha": alpha,
"truncation_point": truncation_point
},
)
def test_beta_coalescent_parameters(self):
for alpha in [1.01, 1.5, 1.99]:
model = msprime.BetaCoalescent(alpha=alpha, truncation_point=1)
assert model.alpha == alpha
assert model.truncation_point == 1
d = model._as_lowlevel()
assert d == {
"name": "beta",
"duration": None,
"alpha": alpha,
"truncation_point": 1,
}
alpha = 1.5
for truncation_point in [0.01, 0.5, 1]:
model = msprime.BetaCoalescent(alpha=alpha,
truncation_point=truncation_point)
assert model.alpha == alpha
assert model.truncation_point == truncation_point
d = model._as_lowlevel()
assert d == {
"name": "beta",
"alpha": alpha,
"truncation_point": truncation_point,
"duration": None,
}
def test_many_models_simulate(self):
Ne = 10000
ts = msprime.simulate(
Ne=Ne,
sample_size=10,
# Use the old-style SimulationModelChange
model=[
"hudson",
msprime.SimulationModelChange(10,
msprime.StandardCoalescent()),
msprime.SimulationModelChange(20,
msprime.SmcApproxCoalescent()),
msprime.SimulationModelChange(
30, msprime.SmcPrimeApproxCoalescent()),
msprime.SimulationModelChange(
40, msprime.DiscreteTimeWrightFisher()),
msprime.SimulationModelChange(
50, msprime.BetaCoalescent(alpha=1.1)),
msprime.SimulationModelChange(60,
msprime.StandardCoalescent()),
],
random_seed=10,
)
for tree in ts.trees():
assert tree.num_roots == 1
def test_beta_coalescent(self):
model = msprime.BetaCoalescent(population_size=5,
alpha=1.5,
truncation_point=10)
ts = msprime.simulate(sample_size=10, model=model)
# TODO real tests
self.assertTrue(ts is not None)
def test_multiple_mergers(self):
for model in [msprime.BetaCoalescent(10), msprime.DiracCoalescent(10)]:
self.assertRaises(_msprime.LibraryError,
msprime.simulate,
10,
model=model,
record_full_arg=True)
def test_many_models(self):
Ne = 10000
ts = msprime.simulate(
Ne=Ne,
sample_size=10,
recombination_rate=0.1,
model=[
"hudson",
msprime.SimulationModelChange(10,
msprime.StandardCoalescent()),
msprime.SimulationModelChange(20,
msprime.SmcApproxCoalescent()),
msprime.SimulationModelChange(
30, msprime.SmcPrimeApproxCoalescent()),
msprime.SimulationModelChange(
40, msprime.DiscreteTimeWrightFisher()),
msprime.SimulationModelChange(
50,
msprime.BetaCoalescent(alpha=1.1, truncation_point=1),
),
msprime.SimulationModelChange(60,
msprime.StandardCoalescent()),
],
random_seed=10,
)
for tree in ts.trees():
self.assertEqual(tree.num_roots, 1)
def test_beta_coalescent(self):
model = msprime.BetaCoalescent(alpha=1, truncation_point=2)
assert model.duration is None
assert model.alpha == 1
assert model.truncation_point == 2
model = msprime.BetaCoalescent(alpha=2, truncation_point=1, duration=3)
assert model.duration == 3
assert model.alpha == 2
assert model.truncation_point == 1
model = msprime.BetaCoalescent()
assert model.duration is None
assert model.alpha is None
with pytest.raises(TypeError, match="takes 1 positional"):
msprime.BetaCoalescent(1)
def test_beta_coalescent_parameters(self):
for alpha in [1.01, 1.5, 1.99]:
model = msprime.BetaCoalescent(alpha, truncation_point=1)
assert model.alpha == alpha
assert model.truncation_point == 1
d = model.get_ll_representation()
assert d == {"name": "beta", "alpha": alpha, "truncation_point": 1}
alpha = 1.5
for truncation_point in [0.01, 0.5, 1]:
model = msprime.BetaCoalescent(alpha, truncation_point)
assert model.alpha == alpha
assert model.truncation_point == truncation_point
d = model.get_ll_representation()
assert d == {
"name": "beta",
"alpha": alpha,
"truncation_point": truncation_point,
}
def test_simulation_model_change(self):
examples = [
msprime.SimulationModelChange(),
msprime.SimulationModelChange(model="hudson"),
msprime.SimulationModelChange(
model=msprime.DiscreteTimeWrightFisher()),
msprime.SimulationModelChange(
model=msprime.BetaCoalescent(alpha=1, truncation_point=2)),
]
self.assert_repr_round_trip(examples)
def test_encode_simulation_models(self):
simple_model = ["hudson", [10, "dtwf"], [20, "smc"], [None, None]]
ts = msprime.simulate(10, model=simple_model)
decoded = self.decode(ts.provenance(0).record)
parameters = decoded.parameters
self.assertEqual(parameters.sample_size, 10)
self.assertEqual(list(parameters.model), simple_model)
model_instances = [
msprime.StandardCoalescent(),
msprime.SimulationModelChange(10,
msprime.DiscreteTimeWrightFisher()),
msprime.SimulationModelChange(20, msprime.SmcApproxCoalescent()),
msprime.SimulationModelChange(30,
msprime.BetaCoalescent(alpha=1.1)),
]
ts = msprime.simulate(10, model=model_instances)
decoded = self.decode(ts.provenance(0).record)
parameters = decoded.parameters
self.assertEqual(parameters.sample_size, 10)
self.assertEqual(parameters.model[0],
{"__class__": "msprime.ancestry.StandardCoalescent"})
self.assertDictEqual(
parameters.model[1],
{
"__class__": "msprime.ancestry.SimulationModelChange",
"model": {
"__class__": "msprime.ancestry.DiscreteTimeWrightFisher"
},
"time": 10,
},
)
self.assertDictEqual(
parameters.model[2],
{
"__class__": "msprime.ancestry.SimulationModelChange",
"model": {
"__class__": "msprime.ancestry.SmcApproxCoalescent"
},
"time": 20,
},
)
self.assertDictEqual(
parameters.model[3],
{
"__class__": "msprime.ancestry.SimulationModelChange",
"model": {
"__class__": "msprime.ancestry.BetaCoalescent",
"alpha": 1.1,
"truncation_point": 1.0,
},
"time": 30,
},
)
def test_simulation_models(self):
examples = [
msprime.StandardCoalescent(),
msprime.SmcApproxCoalescent(),
msprime.SmcPrimeApproxCoalescent(),
msprime.DiscreteTimeWrightFisher(),
msprime.WrightFisherPedigree(),
msprime.BetaCoalescent(),
msprime.BetaCoalescent(alpha=1, truncation_point=10),
msprime.DiracCoalescent(),
msprime.DiracCoalescent(psi=1234, c=56),
msprime.SweepGenicSelection(
position=1,
start_frequency=0.5,
end_frequency=0.9,
alpha=1,
dt=1e-4,
),
]
self.assert_repr_round_trip(examples)
def test_beta_coalescent_parameters(self):
dbl_max = sys.float_info.max
for alpha in [-1, 0, 1.1]:
model = msprime.BetaCoalescent(alpha)
self.assertEqual(model.alpha, alpha)
self.assertEqual(model.truncation_point, dbl_max)
d = model.get_ll_representation()
self.assertEqual(d, {
"name": "beta",
"alpha": alpha,
"truncation_point": dbl_max
})
alpha = 2
for truncation_point in [0, 3, 1e6]:
model = msprime.BetaCoalescent(alpha, truncation_point)
self.assertEqual(model.alpha, alpha)
self.assertEqual(model.truncation_point, truncation_point)
d = model.get_ll_representation()
self.assertEqual(
d, {
"name": "beta",
"alpha": alpha,
"truncation_point": truncation_point
})
def test_simulation_models(self):
simple_model = ["hudson", [10, "dtwf"], [20, "smc"]]
ts = msprime.simulate(10, model=simple_model)
self.verify(ts)
model_instances = [
msprime.StandardCoalescent(),
msprime.SimulationModelChange(10,
msprime.DiscreteTimeWrightFisher()),
msprime.SimulationModelChange(20, msprime.SmcApproxCoalescent()),
msprime.SimulationModelChange(30,
msprime.BetaCoalescent(alpha=1.1)),
]
ts = msprime.simulate(10, model=model_instances)
self.verify(ts)
def test_many_models_sim_ancestry(self):
ts = msprime.sim_ancestry(
samples=10,
population_size=10_000,
model=[
msprime.StandardCoalescent(duration=10),
msprime.SmcApproxCoalescent(duration=10),
msprime.SmcPrimeApproxCoalescent(duration=10),
msprime.DiscreteTimeWrightFisher(duration=10),
msprime.BetaCoalescent(alpha=1.1, duration=10),
msprime.StandardCoalescent(),
],
random_seed=10,
)
for tree in ts.trees():
assert tree.num_roots == 1
def test_model_instances(self):
models = [
msprime.StandardCoalescent(100),
msprime.SmcApproxCoalescent(30),
msprime.SmcPrimeApproxCoalescent(2132),
msprime.DiscreteTimeWrightFisher(500),
msprime.SweepGenicSelection(
reference_size=500, position=0.5, start_frequency=0.1,
end_frequency=0.9, alpha=0.1, dt=0.01),
msprime.DiracCoalescent(),
msprime.BetaCoalescent(),
]
for model in models:
new_model = msprime.model_factory(model=model)
self.assertFalse(new_model is model)
self.assertEqual(new_model.__dict__, model.__dict__)
def test_model_instances(self):
for bad_type in [1234, {}]:
self.assertRaises(TypeError,
msprime.simulator_factory,
sample_size=2,
model=bad_type)
models = [
msprime.StandardCoalescent(),
msprime.SmcApproxCoalescent(),
msprime.SmcPrimeApproxCoalescent(),
msprime.BetaCoalescent(),
msprime.DiracCoalescent(),
]
for model in models:
sim = msprime.simulator_factory(sample_size=10, model=model)
self.assertEqual(sim.get_model(), model)
def test_many_models(self):
Ne = 10000
ts = msprime.simulate(
Ne=Ne,
sample_size=10,
recombination_rate=0.1,
demographic_events=[
msprime.SimulationModelChange(10, msprime.StandardCoalescent(Ne)),
msprime.SimulationModelChange(20, msprime.SmcApproxCoalescent(Ne)),
msprime.SimulationModelChange(30, msprime.SmcPrimeApproxCoalescent(Ne)),
msprime.SimulationModelChange(
40, msprime.DiscreteTimeWrightFisher(100)),
msprime.SimulationModelChange(
50, msprime.BetaCoalescent(reference_size=10)),
msprime.SimulationModelChange(60, msprime.StandardCoalescent(0.1))],
random_seed=10)
for tree in ts.trees():
self.assertEqual(tree.num_roots, 1)
def verify_simulation_models(self, sim_func):
simple_model = ["hudson", [10, "dtwf"], [20, "smc"], [None, None]]
ts = sim_func(10, model=simple_model)
decoded = self.decode(ts.provenance(0).record)
parameters = decoded.parameters
assert list(parameters.model) == simple_model
model_instances = [
msprime.StandardCoalescent(),
msprime.SimulationModelChange(10,
msprime.DiscreteTimeWrightFisher()),
msprime.SimulationModelChange(20, msprime.SmcApproxCoalescent()),
msprime.SimulationModelChange(
30, msprime.BetaCoalescent(alpha=1.1, truncation_point=1)),
]
ts = sim_func(10, model=model_instances)
decoded = self.decode(ts.provenance(0).record)
parameters = decoded.parameters
assert parameters.model[0] == {
"__class__": "msprime.ancestry.StandardCoalescent"
}
assert parameters.model[1] == {
"__class__": "msprime.ancestry.SimulationModelChange",
"model": {
"__class__": "msprime.ancestry.DiscreteTimeWrightFisher"
},
"time": 10,
}
assert parameters.model[2] == {
"__class__": "msprime.ancestry.SimulationModelChange",
"model": {
"__class__": "msprime.ancestry.SmcApproxCoalescent"
},
"time": 20,
}
assert parameters.model[3] == {
"__class__": "msprime.ancestry.SimulationModelChange",
"model": {
"__class__": "msprime.ancestry.BetaCoalescent",
"alpha": 1.1,
"truncation_point": 1.0,
},
"time": 30,
}
def test_many_models_sim_ancestry(self):
ts = msprime.sim_ancestry(
samples=10,
population_size=10_000,
model=[
"hudson",
msprime.AncestryModelChange(10, msprime.StandardCoalescent()),
msprime.AncestryModelChange(20, msprime.SmcApproxCoalescent()),
msprime.AncestryModelChange(
30, msprime.SmcPrimeApproxCoalescent()),
msprime.AncestryModelChange(
40, msprime.DiscreteTimeWrightFisher()),
msprime.AncestryModelChange(50,
msprime.BetaCoalescent(alpha=1.1)),
msprime.AncestryModelChange(60, msprime.StandardCoalescent()),
],
random_seed=10,
)
for tree in ts.trees():
assert tree.num_roots == 1
def test_model_instances(self):
models = [
msprime.StandardCoalescent(),
msprime.SmcApproxCoalescent(),
msprime.SmcPrimeApproxCoalescent(),
msprime.DiscreteTimeWrightFisher(),
msprime.WrightFisherPedigree(),
msprime.SweepGenicSelection(
position=0.5,
start_frequency=0.1,
end_frequency=0.9,
alpha=0.1,
dt=0.01,
),
msprime.BetaCoalescent(alpha=2),
msprime.DiracCoalescent(psi=1, c=1),
]
for model in models:
new_model = msprime.model_factory(model=model)
self.assertTrue(new_model is model)
self.assertEqual(new_model.__dict__, model.__dict__)
def test_reference_size_inherited(self):
for Ne in [1, 10, 100]:
models = [
msprime.DiracCoalescent(psi=0.5, c=0),
msprime.StandardCoalescent(),
msprime.SmcApproxCoalescent(),
msprime.SmcPrimeApproxCoalescent(),
msprime.DiscreteTimeWrightFisher(),
msprime.WrightFisherPedigree(),
msprime.SweepGenicSelection(
position=0.5,
start_frequency=0.1,
end_frequency=0.9,
alpha=0.1,
dt=0.01,
),
msprime.BetaCoalescent(alpha=2),
msprime.DiracCoalescent(psi=1, c=1),
]
for model in models:
new_model = msprime.model_factory(model, reference_size=Ne)
self.assertEqual(new_model.reference_size, Ne)
def test_beta_coalescent(self):
model = msprime.BetaCoalescent(alpha=1, truncation_point=2)
repr_s = "BetaCoalescent(alpha=1, truncation_point=2)"
assert repr(model) == repr_s
assert str(model) == repr_s
def test_beta_coalescent(self):
model = msprime.BetaCoalescent(alpha=1, truncation_point=2)
repr_s = "BetaCoalescent(alpha=1, truncation_point=2)"
self.assertEqual(repr(model), repr_s)
self.assertEqual(str(model), repr_s)
def test_beta_coalescent(self):
model = msprime.BetaCoalescent(alpha=1.5, truncation_point=1)
ts = msprime.simulate(Ne=5, sample_size=10, model=model)
self.assertTrue(all(tree.num_roots == 1 for tree in ts.trees()))
def test_beta_coalescent_integration_fails(self):
model = msprime.BetaCoalescent(population_size=5,
alpha=1e-10,
truncation_point=10)
with self.assertRaises(_msprime.LibraryError):
msprime.simulate(sample_size=10, model=model)
def test_beta_coalescent(self):
model = msprime.BetaCoalescent(5, 10)
ts = msprime.simulate(sample_size=10, model=model)
# TODO real tests
self.assertTrue(ts is not None)
def test_beta_coalescent(self):
model = msprime.BetaCoalescent(alpha=1.5)
ts = msprime.simulate(Ne=5, sample_size=10, model=model)
assert all(tree.num_roots == 1 for tree in ts.trees())