def test_model5_translation(self):
N_a, nu1B, nu1, nu1F, nu2B, nu2F, t1, t2, t3 = self.get_genetic_variables_model3(
)
t4 = TimeVariable('t4', units="genetic")
var2values = {
'N_a': 1e5,
'nu1B': 0.4,
'nu1': 0.8,
'nu1F': 0.1,
'nu2B': 0.5,
'nu2F': 0.2,
't1': 2,
't2': 3,
't3': 4,
't4': 5
}
m = TreeDemographicModel(gen_time=29, mutation_rate=1.25e-8)
m.add_leaf(0, size_pop=nu1F)
m.add_leaf(1, size_pop=nu2F)
m.change_pop_size(0, t=t1, size_pop=nu1)
m.change_pop_size(0, t=t3, size_pop=nu1B)
m.change_pop_size(1, t=t2, size_pop=nu2B)
m.move_lineages(1, 0, t=t4, size_pop=N_a)
translated_model = m.translate_to(EpochDemographicModel, var2values)
em = EpochDemographicModel(gen_time=29, mutation_rate=1.25e-8)
em.add_split(0, [nu1B, nu2B])
em.add_epoch(operation_creation(Subtraction, t4, t3), [nu1B, nu2B])
em.add_epoch(operation_creation(Subtraction, t3, t2), [nu1, nu2B])
em.add_epoch(operation_creation(Subtraction, t2, t1), [nu1, nu2F])
em.add_epoch(operation_creation(Subtraction, t1, 0), [nu1F, nu2F])
self.assertEqual(2, translated_model.number_of_populations())
self.assertEqual(translated_model, em)
def test_model2_translation(self):
N_a, nu1, nu2, nu2F, t1, t2 = self.get_genetic_variables_model1()
var2values = {
'nu1': 0.4,
'nu2F': 0.7,
'nu2': 0.5,
'N_a': 1e5,
't1': 1,
't2': 5
}
m = TreeDemographicModel(gen_time=29, mutation_rate=1.25e-8)
m.add_leaf(0, size_pop=nu1)
m.add_leaf(1, size_pop=nu2F)
m.change_pop_size(1, t=t1, size_pop=nu2, dyn="Exp", g=0.9)
m.move_lineages(1, 0, t=t2, size_pop=N_a)
em = EpochDemographicModel(gen_time=29, mutation_rate=1.25e-8)
# g = log(N / N0) / t where N is final size (closer to nowdays) and
# N0 is start size (the most ancient) t - time interval
# THEN we have g, t and N and we want N0 = N / exp(gt)
exp_op = operation_creation(
Exp,
operation_creation(Multiplication, 0.9,
operation_creation(Subtraction, t2, t1)))
nu20 = operation_creation(Division, nu2, exp_op)
# Construct our model
em.add_split(0, [nu1, nu20])
em.add_epoch(operation_creation(Subtraction, t2, t1), [nu1, nu2],
dyn_args=['Sud', "Exp"])
em.add_epoch(operation_creation(Subtraction, t1, 0), [nu1, nu2F])
translated_model = m.translate_to(EpochDemographicModel, var2values)
def test_model1_translation(self):
N_a, nu1, nu2, nu2F, t1, t2 = self.get_genetic_variables_model1()
var2values = {
'nu1': 0.4,
'nu2F': 0.7,
'nu2': 0.5,
'N_a': 1e5,
't1': 1,
't2': 5
}
m = TreeDemographicModel(gen_time=29, mutation_rate=1.25e-8)
m.add_leaf(0, size_pop=nu1)
m.add_leaf(1, size_pop=nu2F)
m.change_pop_size(1, t=t1, size_pop=nu2)
m.move_lineages(1, 0, t=t2, size_pop=N_a)
self.assertEqual(m.number_of_populations(), 2)
translated_model = EpochDemographicModel.create_from(m, var2values)
em = EpochDemographicModel(gen_time=29, mutation_rate=1.25e-8)
em.add_split(0, [nu1, nu2])
em.add_epoch(operation_creation(Subtraction, t2, t1), [nu1, nu2])
em.add_epoch(operation_creation(Subtraction, t1, 0), [nu1, nu2F])
self.assertEqual(translated_model, em)