def testBDTree(self):
"""PureCoalescentTreeTest -- tree generation without checking [TODO: checks]"""
_RNG = MockRandom()
for num_leaves in range(2, 20):
t = birthdeath.birth_death_tree(birth_rate=1.0, death_rate=0.2, ntax=num_leaves, rng=_RNG)
self.assertTrue(t._debug_tree_is_valid())
self.assertEqual(num_leaves, len(t.leaf_nodes()))
def testGSA(self):
"""test that the pure-birth process produces the correct number of tips with GSA."""
_RNG = MockRandom()
for num_leaves in range(2, 20):
t = birthdeath.birth_death_tree(birth_rate=1.0, death_rate=0.0, ntax=num_leaves, gsa_ntax=4*num_leaves, rng=_RNG)
self.assertTrue(t._debug_tree_is_valid())
self.assertEqual(num_leaves, len(t.leaf_nodes()))
def testGSA(self):
"""test that the pure-birth process produces the correct number of tips with GSA."""
_RNG = MockRandom()
for num_leaves in range(2, 20):
t = birthdeath.birth_death_tree(birth_rate=1.0, death_rate=0.0, num_extant_tips=num_leaves, gsa_ntax=4*num_leaves, rng=_RNG)
self.assertTrue(t._debug_tree_is_valid())
self.assertEqual(num_leaves, len(t.leaf_nodes()))
def testBDTree(self):
"""PureCoalescentTreeTest -- tree generation without checking [TODO: checks]"""
_RNG = MockRandom()
for num_leaves in range(2, 20):
t = birthdeath.birth_death_tree(birth_rate=1.0, death_rate=0.2, num_extant_tips=num_leaves, rng=_RNG)
self.assertTrue(t._debug_tree_is_valid())
self.assertEqual(num_leaves, len(t.leaf_nodes()))
def evolve_to_current_time(node, finalize=False):
viruses = [virus for virus in node.viruses()]
for virus in viruses:
time = GC.time - virus.get_time()
if time > 0:
node.remove_virus(virus)
success = False
for _ in range(100):
tree = birth_death_tree(GC.bd_birth,
GC.bd_death,
birth_rate_sd=GC.bd_birth_sd,
death_rate_sd=GC.bd_death_sd,
max_time=time,
repeat_until_success=True,
rng=rng)
if tree.seed_node.num_child_nodes() > 1:
success = True
break
assert success, "Failed to create non-empty Birth-Death tree after 100 attempts. Perhaps try a higher birth rate or lower death rate?"
virus.set_time(virus.get_time() + tree.seed_node.edge_length)
for c in tree.seed_node.child_node_iter():
GC.treenode_add_child(virus, c, node)
