def generate_single_labeled_history(tree,
pop_size=None,
rng=None):
# get collection of nodes organized by the order
# of coalescence as given by the level
node_event_order = {}
event_nodes = {}
num_leaves = 0
for nd in tree.postorder_node_iter():
if nd.is_leaf():
node_event_order[nd] = 0
num_leaves += 1
else:
eo = max([node_event_order[ch] for ch in nd.child_nodes()]) + 1
node_event_order[nd] = eo
try:
event_nodes[node_event_order[nd]].append(nd)
except KeyError:
event_nodes[node_event_order[nd]] = [nd]
# set the node ages
node_ages = {}
event_idx_list = sorted(event_nodes.keys())
for nd in event_nodes[0]:
node_ages[nd] = 0.0
current_tree_max_age = 0.0
num_nodes_remaining = num_leaves
for event_idx in event_idx_list[1:]:
for nd in event_nodes[event_idx]:
child_nodes = nd.child_nodes()
max_ch_age = max([node_ages[ch] for ch in child_nodes])
min_age = max(current_tree_max_age, max_ch_age)
if rng is None:
# rng is not given: use expected waiting time
wt = coalescent.expected_tmrca(
n_genes=num_nodes_remaining,
pop_size=pop_size,
n_to_coalesce=len(child_nodes))
else:
# rng is given: draw random waiting time
wt = coalescent.time_to_coalescence(
n_genes=num_nodes_remaining,
pop_size=pop_size,
n_to_coalesce=len(child_nodes))
node_ages[nd] = min_age + wt
current_tree_max_age += wt
num_nodes_remaining = num_nodes_remaining - len(child_nodes) + 1
# set the edge lengths according to the node ages
for nd in tree.preorder_node_iter():
if nd.parent_node is None:
nd.edge.length = 0.0
else:
nd.edge.length = node_ages[nd.parent_node] - node_ages[nd]
return tree
def generate_single_labeled_history(tree, pop_size=None, rng=None):
# get collection of nodes organized by the order
# of coalescence as given by the level
node_event_order = {}
event_nodes = {}
num_leaves = 0
for nd in tree.postorder_node_iter():
if nd.is_leaf():
node_event_order[nd] = 0
num_leaves += 1
else:
eo = max([node_event_order[ch] for ch in nd.child_nodes()]) + 1
node_event_order[nd] = eo
try:
event_nodes[node_event_order[nd]].append(nd)
except KeyError:
event_nodes[node_event_order[nd]] = [nd]
# set the node ages
node_ages = {}
event_idx_list = sorted(event_nodes.keys())
for nd in event_nodes[0]:
node_ages[nd] = 0.0
current_tree_max_age = 0.0
num_nodes_remaining = num_leaves
for event_idx in event_idx_list[1:]:
for nd in event_nodes[event_idx]:
child_nodes = nd.child_nodes()
max_ch_age = max([node_ages[ch] for ch in child_nodes])
min_age = max(current_tree_max_age, max_ch_age)
if rng is None:
# rng is not given: use expected waiting time
wt = coalescent.expected_tmrca(n_genes=num_nodes_remaining,
pop_size=pop_size,
n_to_coalesce=len(child_nodes))
else:
# rng is given: draw random waiting time
wt = coalescent.time_to_coalescence(
n_genes=num_nodes_remaining,
pop_size=pop_size,
n_to_coalesce=len(child_nodes))
node_ages[nd] = min_age + wt
current_tree_max_age += wt
num_nodes_remaining = num_nodes_remaining - len(child_nodes) + 1
# set the edge lengths according to the node ages
for nd in tree.preorder_node_iter():
if nd.parent_node is None:
nd.edge.length = 0.0
else:
nd.edge.length = node_ages[nd.parent_node] - node_ages[nd]
return tree
def _generate_labeled_history(tree,
coal_event_list,
num_leaves=None,
pop_size=None,
rng=None):
# set the node ages
node_ages = {}
for nd in coal_event_list[0]:
node_ages[nd] = 0.0
current_tree_max_age = 0.0
if num_leaves is None:
num_nodes_remaining = num_leaves
else:
num_nodes_remaining = len([lf for lf in tree.leaf_iter()])
# process events in order of occurrence
for event_nodes in coal_event_list[1:]:
for nd in event_nodes:
child_nodes = nd.child_nodes()
max_ch_age = max([node_ages[ch] for ch in child_nodes])
min_age = max(current_tree_max_age, max_ch_age)
if rng is None:
# rng is not given: use expected waiting time
wt = coalescent.expected_tmrca(
n_genes=num_nodes_remaining,
pop_size=pop_size,
n_to_coalesce=len(child_nodes))
else:
# rng is given: draw random waiting time
wt = coalescent.time_to_coalescence(
n_genes=num_nodes_remaining,
pop_size=pop_size,
n_to_coalesce=len(child_nodes))
node_ages[nd] = min_age + wt
current_tree_max_age += wt
num_nodes_remaining = num_nodes_remaining - len(child_nodes) + 1
# set the edge lengths according to the node ages
for nd in tree.preorder_node_iter():
if nd.parent_node is None:
nd.edge.length = 0.0
else:
nd.edge.length = node_ages[nd.parent_node] - node_ages[nd]
return tree
def _generate_labeled_history(tree,
coal_event_list,
num_leaves=None,
pop_size=None,
rng=None):
# set the node ages
node_ages = {}
for nd in coal_event_list[0]:
node_ages[nd] = 0.0
current_tree_max_age = 0.0
if num_leaves is None:
num_nodes_remaining = num_leaves
else:
num_nodes_remaining = len([lf for lf in tree.leaf_iter()])
# process events in order of occurrence
for event_nodes in coal_event_list[1:]:
for nd in event_nodes:
child_nodes = nd.child_nodes()
max_ch_age = max([node_ages[ch] for ch in child_nodes])
min_age = max(current_tree_max_age, max_ch_age)
if rng is None:
# rng is not given: use expected waiting time
wt = coalescent.expected_tmrca(n_genes=num_nodes_remaining,
pop_size=pop_size,
n_to_coalesce=len(child_nodes))
else:
# rng is given: draw random waiting time
wt = coalescent.time_to_coalescence(
n_genes=num_nodes_remaining,
pop_size=pop_size,
n_to_coalesce=len(child_nodes))
node_ages[nd] = min_age + wt
current_tree_max_age += wt
num_nodes_remaining = num_nodes_remaining - len(child_nodes) + 1
# set the edge lengths according to the node ages
for nd in tree.preorder_node_iter():
if nd.parent_node is None:
nd.edge.length = 0.0
else:
nd.edge.length = node_ages[nd.parent_node] - node_ages[nd]
return tree
