def test_call_exact(self):
"""BirthDeathModel call should produce right # taxa when exact"""
m = BirthDeathModel(0.01, 0.005, 0.1, MaxTaxa=10)
for i in range(10):
try:
result = m(filter=True, exact=True)
self.assertEqual(len(list(result.traverse())), 10)
except (TooManyTaxaError, ExtinctionError), e:
pass
def test_timeOk(self):
"""BirthDeathModel TimeOk should return True if time not exceeded"""
b = BirthDeathModel(0.1, 0.2, 0.3, MaxStep=5)
assert b.timeOk()
b.CurrStep = 4
assert b.timeOk()
b.CurrStep = 5
assert not b.timeOk()
b.CurrStep = 1000
assert not b.timeOk()
b.MaxStep = None
assert b.timeOk()
b.MaxStep = 1001
assert b.timeOk()
b.step()
assert not b.timeOk()
def test_init_extras(self):
"""BirthDeathModel should init OK with extra params"""
m = BirthDeathModel(BirthProb=0.1, DeathProb=0.2, TimePerStep=0.3, \
ChangedBirthProb=0.4, ChangedDeathProb=0.3, ChangedBirthStep=3,\
ChangedDeathStep=4, MaxStep=5, MaxTaxa=10)
self.assertEqual(m.BirthProb, 0.1)
self.assertEqual(m.DeathProb, 0.2)
self.assertEqual(m.TimePerStep, 0.3)
self.assertEqual(m.ChangedBirthProb, 0.4)
self.assertEqual(m.ChangedDeathProb, 0.3)
self.assertEqual(m.ChangedBirthStep, 3)
self.assertEqual(m.ChangedDeathStep, 4)
self.assertEqual(m.MaxStep, 5)
self.assertEqual(m.MaxTaxa, 10)
self.assertEqual(m.CurrStep, 0)
self.assertEqual(m.Tree.__class__, m.NodeClass)
self.assertEqual(m.CurrTaxa, [m.Tree])
def test_init_deafults(self):
"""BirthDeathModel should init correctly w/ default params"""
m = BirthDeathModel(0.1, 0.2, 0.3)
self.assertEqual(m.BirthProb, 0.1)
self.assertEqual(m.DeathProb, 0.2)
self.assertEqual(m.TimePerStep, 0.3)
self.assertEqual(m.MaxStep, 1000)
self.assertEqual(m.MaxTaxa, None)
self.assertEqual(m.CurrStep, 0)
self.assertEqual(m.Tree.__class__, m.NodeClass)
self.assertEqual(m.CurrTaxa, [m.Tree])
self.assertEqual(m.ChangedBirthProb, None)
self.assertEqual(m.ChangedDeathProb, None)
self.assertEqual(m.ChangedBirthStep, None)
self.assertEqual(m.ChangedDeathStep, None)
self.assertEqual(m.CurrBirthProb, 0.1)
self.assertEqual(m.CurrDeathProb, 0.2)
def test_step(self):
"""BirthDeathModel step should match hand-calculated results"""
m = BirthDeathModel(BirthProb=0.1, DeathProb=0.2, TimePerStep=1)
born_and_died = FakeRandom([0], True)
born_only = FakeRandom([1, 0], True)
died_only = FakeRandom([0, 1], True)
neither = FakeRandom([1], True)
kill_alternate = FakeRandom([0, 1, 1, 1], True)
born_alternate = FakeRandom([1, 1, 1, 0], True)
#check that with neither birth nor death, we just continue
m.step(neither)
self.assertEqual(len(m.Tree.Children), 0)
#check that with born_only we get a duplication
m.step(born_only)
self.assertEqual(len(m.Tree.Children), 2)
assert m.Tree not in m.CurrTaxa
for i in m.CurrTaxa:
assert i.Parent is m.Tree
self.assertEqual(i.Length, 1)
#check that with a second round of born_only we duplicate again
m.step(born_only)
self.assertEqual(len(m.Tree.Children), 2)
self.assertEqual(len(list(m.Tree.traverse())), 4)
for i in m.Tree.traverse():
self.assertEqual(i.Length, 1)
for i in m.Tree.Children:
self.assertEqual(i.Length, 1)
#check that branch lengths add correctly
for i in range(4):
m.step(neither)
self.assertEqual(len(m.CurrTaxa), 4)
self.assertEqual(len(m.Tree.Children), 2)
self.assertEqual(len(list(m.Tree.traverse())), 4)
for i in m.Tree.traverse():
self.assertEqual(i.Length, 5)
for i in m.Tree.Children:
self.assertEqual(i.Length, 1)
#check that we can kill offspring correctly
m.step(kill_alternate)
self.assertEqual(len(m.CurrTaxa), 2)
#make sure we killed the right children
m.Tree.assignIds()
for i in m.Tree.Children:
#note that killing a child doesn't remove it, just stops it changing
self.assertEqual(len(i.Children), 2)
self.assertEqual(i.Children[0].Length, 5)
self.assertEqual(i.Children[1].Length, 6)
self.assertEqual([i.Length for i in m.Tree.traverse()], \
[5,6,5,6])
#make sure that born_and_died does the same thing as neither
m.step(born_and_died)
self.assertEqual([i.Length for i in m.Tree.traverse()], \
[5,7,5,7])
m.step(neither)
self.assertEqual([i.Length for i in m.Tree.traverse()], \
[5,8,5,8])
#check that only CurrTaxa are brought forward
self.assertEqual([i.Length for i in m.CurrTaxa], [8, 8])
#check that we can duplicate a particular taxon
m.step(born_alternate)
self.assertEqual([i.Length for i in m.CurrTaxa], [9, 1, 1])
self.assertEqual(m.CurrTaxa[1].Parent.Length, 8)
#check that we can kill 'em all
m.step(died_only)
self.assertEqual(len(m.CurrTaxa), 0)
