def coalesce(nodes,
pop_size=None,
period=None,
rng=None,
use_expected_tmrca=False):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.coalescent' module has moved to 'dendropy.model.coalescent', and this function has been renamed 'coalesce_nodes'.",
old_construct="from dendropy import coalescent\ncoalescent.coalesce(...)",
new_construct="from dendropy.model import coalescent\ncoalescent.coalesce_nodes(...)")
return coalescent.coalesce_nodes(
nodes=nodes,
pop_size=pop_size,
period=period,
rng=rng,
use_expected_tmrca=use_expected_tmrca)
def simulate_contained_kingman(self,
edge_pop_size_attr='pop_size',
default_pop_size=1,
label=None,
rng=None,
use_expected_tmrca=False):
"""
Simulates and returns a "censored" (Kingman) neutral coalescence tree
conditional on self.
``rng``
Random number generator to use. If |None|, the default will
be used.
``edge_pop_size_attr``
Name of attribute of self's edges that specify the population
size. If this attribute does not exist, then the population
size is taken to be 1.
Note that all edge-associated taxon sets must be up-to-date (otherwise,
``build_edge_taxa_sets()`` should be called), and that the tree
is *not* added to the set of contained trees. For the latter, call
``embed_contained_kingman``.
"""
# Dictionary that maps nodes of containing tree to list of
# corresponding nodes on gene tree, initially populated with leaf
# nodes.
contained_nodes = {}
for nd in self.leaf_node_iter():
contained_nodes[nd] = []
for gt in nd.edge.contained_taxa:
gn = dendropy.Node(taxon=gt)
contained_nodes[nd].append(gn)
# Generate the tree structure
for edge in self.postorder_edge_iter():
if edge.head_node.parent_node is None:
# root: run unconstrained coalescence until just one gene node
# remaining
if hasattr(edge, edge_pop_size_attr):
pop_size = getattr(edge, edge_pop_size_attr)
else:
pop_size = default_pop_size
if len(contained_nodes[edge.head_node]) > 1:
final = coalescent.coalesce_nodes(nodes=contained_nodes[edge.head_node],
pop_size=pop_size,
period=None,
rng=rng,
use_expected_tmrca=use_expected_tmrca)
else:
final = contained_nodes[edge.head_node]
else:
# run until next coalescence event, as determined by this edge
# size.
if hasattr(edge, edge_pop_size_attr):
pop_size = getattr(edge, edge_pop_size_attr)
else:
pop_size = default_pop_size
remaining = coalescent.coalesce_nodes(nodes=contained_nodes[edge.head_node],
pop_size=pop_size,
period=edge.length,
rng=rng,
use_expected_tmrca=use_expected_tmrca)
try:
contained_nodes[edge.tail_node].extend(remaining)
except KeyError:
contained_nodes[edge.tail_node] = remaining
# Create and return the full tree
contained_tree = dendropy.Tree(taxon_namespace=self.contained_taxon_namespace, label=label)
contained_tree.seed_node = final[0]
contained_tree.is_rooted = True
return contained_tree
def simulate_contained_kingman(self,
edge_pop_size_attr='pop_size',
default_pop_size=1,
label=None,
rng=None,
use_expected_tmrca=False):
"""
Simulates and returns a "censored" (Kingman) neutral coalescence tree
conditional on self.
``rng``
Random number generator to use. If |None|, the default will
be used.
``edge_pop_size_attr``
Name of attribute of self's edges that specify the population
size. If this attribute does not exist, then the population
size is taken to be 1.
Note that all edge-associated taxon sets must be up-to-date (otherwise,
``build_edge_taxa_sets()`` should be called), and that the tree
is *not* added to the set of contained trees. For the latter, call
``embed_contained_kingman``.
"""
# Dictionary that maps nodes of containing tree to list of
# corresponding nodes on gene tree, initially populated with leaf
# nodes.
contained_nodes = {}
for nd in self.leaf_node_iter():
contained_nodes[nd] = []
for gt in nd.edge.contained_taxa:
gn = dendropy.Node(taxon=gt)
contained_nodes[nd].append(gn)
# Generate the tree structure
for edge in self.postorder_edge_iter():
if edge.head_node.parent_node is None:
# root: run unconstrained coalescence until just one gene node
# remaining
if hasattr(edge, edge_pop_size_attr):
pop_size = getattr(edge, edge_pop_size_attr)
else:
pop_size = default_pop_size
if len(contained_nodes[edge.head_node]) > 1:
final = coalescent.coalesce_nodes(
nodes=contained_nodes[edge.head_node],
pop_size=pop_size,
period=None,
rng=rng,
use_expected_tmrca=use_expected_tmrca)
else:
final = contained_nodes[edge.head_node]
else:
# run until next coalescence event, as determined by this edge
# size.
if hasattr(edge, edge_pop_size_attr):
pop_size = getattr(edge, edge_pop_size_attr)
else:
pop_size = default_pop_size
remaining = coalescent.coalesce_nodes(
nodes=contained_nodes[edge.head_node],
pop_size=pop_size,
period=edge.length,
rng=rng,
use_expected_tmrca=use_expected_tmrca)
try:
contained_nodes[edge.tail_node].extend(remaining)
except KeyError:
contained_nodes[edge.tail_node] = remaining
# Create and return the full tree
contained_tree = dendropy.Tree(
taxon_namespace=self.contained_taxon_namespace, label=label)
contained_tree.seed_node = final[0]
contained_tree.is_rooted = True
return contained_tree