def _generate_lineages(self, **kwargs):
current_time = 0.0
lineage_data = kwargs.get("lineage_data")
max_time = kwargs.get("max_time", None)
num_extant_lineages = kwargs.get("num_extant_lineages", None)
num_extant_orthospecies = kwargs.get("num_extant_orthospecies", None)
phase_idx = kwargs.get("phase_idx")
lineage_taxon_namespace = kwargs.get("lineage_taxon_namespace", None)
species_taxon_namespace = kwargs.get("species_taxon_namespace", None)
if phase_idx == 0:
lineage_data[phase_idx]["lineage_id"] = 1
lineage_data[phase_idx]["species_id"] = 1
initial_lineage = self._new_lineage(
lineage_id=lineage_data[phase_idx]["lineage_id"],
parent_lineage=None,
origin_time=-1e-10,
)
lineage_data[phase_idx]["orthospecies_lineages"] = [
initial_lineage
]
lineage_data[phase_idx]["incipient_species_lineages"] = []
else:
lineage_data[phase_idx]["lineage_id"] = lineage_data[0].get(
"lineage_id", 0) + 1
lineage_data[phase_idx]["species_id"] = lineage_data[0].get(
"species_id", 0)
initial_lineage = self._new_lineage(
lineage_id=lineage_data[phase_idx]["lineage_id"],
parent_lineage=lineage_data[0]["lineage_collection"][0],
origin_time=current_time,
)
lineage_data[phase_idx]["orthospecies_lineages"] = []
lineage_data[phase_idx]["incipient_species_lineages"] = [
initial_lineage
]
lineage_data[phase_idx]["lineage_collection"] = [initial_lineage]
lineage_collection = lineage_data[phase_idx]["lineage_collection"]
orthospecies_lineages = lineage_data[phase_idx][
"orthospecies_lineages"]
incipient_species_lineages = lineage_data[phase_idx][
"incipient_species_lineages"]
while True:
num_orthospecies = len(orthospecies_lineages)
num_incipient_species = len(incipient_species_lineages)
if num_incipient_species + num_orthospecies == 0:
raise TreeSimTotalExtinctionException()
## Draw time to next event
event_rates = []
# Event type 0
event_rates.append(
self.speciation_initiation_from_orthospecies_rate *
num_orthospecies)
# Event type 1
event_rates.append(self.orthospecies_extinction_rate *
num_orthospecies)
# Event type 2
event_rates.append(
self.speciation_initiation_from_incipient_species_rate *
num_incipient_species)
# Event type 3
event_rates.append(self.speciation_completion_rate *
num_incipient_species)
# Event type 4
event_rates.append(self.incipient_species_extinction_rate *
num_incipient_species)
# All events
rate_of_any_event = sum(event_rates)
# Waiting time
waiting_time = self.rng.expovariate(rate_of_any_event)
# waiting_time = -math.log(self.rng.uniform(0, 1))/rate_of_any_event
if max_time and (current_time + waiting_time) > max_time:
current_time = max_time
break
# we do this here so that the (newest) tip lineages have the
# waiting time to the next event branch lengths
if num_extant_lineages is not None and (
num_incipient_species +
num_orthospecies) >= num_extant_lineages:
final_time = current_time + self.rng.uniform(0, waiting_time)
lineage_data[phase_idx]["final_time"] = final_time
break
elif num_extant_orthospecies is not None:
## note: very expensive operation to count orthospecies leaves!
final_time = current_time + self.rng.uniform(0, waiting_time)
lineage_collection_snapshot = [
lineage.clone() for lineage in itertools.chain(
lineage_data[0]["lineage_collection"], lineage_data[1]
["lineage_collection"])
]
try:
orthospecies_tree = self._compile_species_tree(
lineage_collection=lineage_collection_snapshot,
max_time=final_time,
)
num_leaves = len(orthospecies_tree.leaf_nodes())
if num_leaves >= num_extant_orthospecies:
lineage_tree = self._compile_lineage_tree(
lineage_collection=lineage_collection_snapshot,
max_time=final_time,
is_drop_extinct=True,
)
lineage_tree, orthospecies_tree = self._finalize_trees(
lineage_tree=lineage_tree,
lineage_taxon_namespace=lineage_taxon_namespace,
orthospecies_tree=orthospecies_tree,
species_taxon_namespace=species_taxon_namespace,
lineage_collection=lineage_collection_snapshot,
)
lineage_data[phase_idx]["lineage_tree"] = lineage_tree
lineage_data[phase_idx][
"orthospecies_tree"] = orthospecies_tree
return
except ProcessFailedException:
pass
# add to current time
current_time += waiting_time
# Select event
event_type_idx = probability.weighted_index_choice(
weights=event_rates, rng=self.rng)
assert (event_type_idx >= 0 and event_type_idx <= 4)
if event_type_idx == 0:
# Splitting of new incipient species lineage from orthospecies lineage
parent_lineage = self.rng.choice(orthospecies_lineages)
lineage_data[phase_idx]["lineage_id"] += 1
new_lineage = self._new_lineage(
lineage_id=lineage_data[phase_idx]["lineage_id"],
parent_lineage=parent_lineage,
origin_time=current_time,
)
lineage_collection.append(new_lineage)
incipient_species_lineages.append(new_lineage)
elif event_type_idx == 1:
# Extinction of an orthospecies lineage
lineage_idx = self.rng.randint(0,
len(orthospecies_lineages) - 1)
orthospecies_lineages[
lineage_idx].extinction_time = current_time
del orthospecies_lineages[lineage_idx]
elif event_type_idx == 2:
# Splitting of new incipient species lineage from incipient lineage
parent_lineage = self.rng.choice(incipient_species_lineages)
lineage_data[phase_idx]["lineage_id"] += 1
new_lineage = self._new_lineage(
lineage_id=lineage_data[phase_idx]["lineage_id"],
parent_lineage=parent_lineage,
origin_time=current_time,
)
lineage_collection.append(new_lineage)
incipient_species_lineages.append(new_lineage)
elif event_type_idx == 3:
# Completion of speciation
lineage_idx = self.rng.randint(
0,
len(incipient_species_lineages) - 1)
lineage = incipient_species_lineages[lineage_idx]
lineage.speciation_completion_time = current_time
lineage_data[phase_idx]["species_id"] += 1
lineage.species_id = lineage_data[phase_idx]["species_id"]
orthospecies_lineages.append(lineage)
del incipient_species_lineages[lineage_idx]
elif event_type_idx == 4:
# Extinction of an incipient_species lineage
lineage_idx = self.rng.randint(
0,
len(incipient_species_lineages) - 1)
incipient_species_lineages[
lineage_idx].extinction_time = current_time
del incipient_species_lineages[lineage_idx]
else:
raise Exception(
"Unexpected event type index: {}".format(event_type_idx))
def _generate_lineages(self, **kwargs):
current_time = 0.0
lineage_data = kwargs.get("lineage_data")
max_time = kwargs.get("max_time", None)
num_extant_lineages = kwargs.get("num_extant_lineages", None)
num_extant_orthospecies = kwargs.get("num_extant_orthospecies", None)
phase_idx = kwargs.get("phase_idx")
lineage_taxon_namespace = kwargs.get("lineage_taxon_namespace", None)
species_taxon_namespace = kwargs.get("species_taxon_namespace", None)
if phase_idx == 0:
lineage_data[phase_idx]["lineage_id"] = 1
lineage_data[phase_idx]["species_id"] = 1
initial_lineage = self._new_lineage(
lineage_id=lineage_data[phase_idx]["lineage_id"],
parent_lineage=None,
origin_time=-1e-10,
)
lineage_data[phase_idx]["orthospecies_lineages"] = [initial_lineage]
lineage_data[phase_idx]["incipient_species_lineages"] = []
else:
lineage_data[phase_idx]["lineage_id"] = lineage_data[0].get("lineage_id", 0) + 1
lineage_data[phase_idx]["species_id"] = lineage_data[0].get("species_id", 0)
initial_lineage = self._new_lineage(
lineage_id=lineage_data[phase_idx]["lineage_id"],
parent_lineage=lineage_data[0]["lineage_collection"][0],
origin_time=current_time,
)
lineage_data[phase_idx]["orthospecies_lineages"] = []
lineage_data[phase_idx]["incipient_species_lineages"] = [initial_lineage]
lineage_data[phase_idx]["lineage_collection"] = [initial_lineage]
lineage_collection = lineage_data[phase_idx]["lineage_collection"]
orthospecies_lineages = lineage_data[phase_idx]["orthospecies_lineages"]
incipient_species_lineages = lineage_data[phase_idx]["incipient_species_lineages"]
while True:
num_orthospecies = len(orthospecies_lineages)
num_incipient_species = len(incipient_species_lineages)
if num_incipient_species + num_orthospecies == 0:
raise TreeSimTotalExtinctionException()
## Draw time to next event
event_rates = []
# Event type 0
event_rates.append(self.speciation_initiation_from_orthospecies_rate * num_orthospecies)
# Event type 1
event_rates.append(self.orthospecies_extinction_rate * num_orthospecies)
# Event type 2
event_rates.append(self.speciation_initiation_from_incipient_species_rate * num_incipient_species)
# Event type 3
event_rates.append(self.speciation_completion_rate * num_incipient_species)
# Event type 4
event_rates.append(self.incipient_species_extinction_rate * num_incipient_species)
# All events
rate_of_any_event = sum(event_rates)
# Waiting time
waiting_time = self.rng.expovariate(rate_of_any_event)
# waiting_time = -math.log(self.rng.uniform(0, 1))/rate_of_any_event
if max_time and (current_time + waiting_time) > max_time:
current_time = max_time
break
# we do this here so that the (newest) tip lineages have the
# waiting time to the next event branch lengths
if num_extant_lineages is not None and (num_incipient_species + num_orthospecies) >= num_extant_lineages:
final_time = current_time + self.rng.uniform(0, waiting_time)
lineage_data[phase_idx]["final_time"] = final_time
break
elif num_extant_orthospecies is not None:
## note: very expensive operation to count orthospecies leaves!
final_time = current_time + self.rng.uniform(0, waiting_time)
lineage_collection_snapshot = [lineage.clone() for lineage in itertools.chain(lineage_data[0]["lineage_collection"], lineage_data[1]["lineage_collection"])]
try:
orthospecies_tree = self._compile_species_tree(
lineage_collection=lineage_collection_snapshot,
max_time=final_time,
)
num_leaves = len(orthospecies_tree.leaf_nodes())
if num_leaves >= num_extant_orthospecies:
lineage_tree = self._compile_lineage_tree(
lineage_collection=lineage_collection_snapshot,
max_time=final_time,
is_drop_extinct=True,
)
lineage_tree, orthospecies_tree = self._finalize_trees(
lineage_tree=lineage_tree,
lineage_taxon_namespace=lineage_taxon_namespace,
orthospecies_tree=orthospecies_tree,
species_taxon_namespace=species_taxon_namespace,
lineage_collection=lineage_collection_snapshot,
)
lineage_data[phase_idx]["lineage_tree"] = lineage_tree
lineage_data[phase_idx]["orthospecies_tree"] = orthospecies_tree
return
except ProcessFailedException:
pass
# add to current time
current_time += waiting_time
# Select event
event_type_idx = probability.weighted_index_choice(weights=event_rates, rng=self.rng)
assert (event_type_idx >= 0 and event_type_idx <= 4)
if event_type_idx == 0:
# Splitting of new incipient species lineage from orthospecies lineage
parent_lineage = self.rng.choice(orthospecies_lineages)
lineage_data[phase_idx]["lineage_id"] += 1
new_lineage = self._new_lineage(
lineage_id=lineage_data[phase_idx]["lineage_id"],
parent_lineage=parent_lineage,
origin_time=current_time,
)
lineage_collection.append(new_lineage)
incipient_species_lineages.append(new_lineage)
elif event_type_idx == 1:
# Extinction of an orthospecies lineage
lineage_idx = self.rng.randint(0, len(orthospecies_lineages)-1)
orthospecies_lineages[lineage_idx].extinction_time = current_time
del orthospecies_lineages[lineage_idx]
elif event_type_idx == 2:
# Splitting of new incipient species lineage from incipient lineage
parent_lineage = self.rng.choice(incipient_species_lineages)
lineage_data[phase_idx]["lineage_id"] += 1
new_lineage = self._new_lineage(
lineage_id=lineage_data[phase_idx]["lineage_id"],
parent_lineage=parent_lineage,
origin_time=current_time,
)
lineage_collection.append(new_lineage)
incipient_species_lineages.append(new_lineage)
elif event_type_idx == 3:
# Completion of speciation
lineage_idx = self.rng.randint(0, len(incipient_species_lineages)-1)
lineage = incipient_species_lineages[lineage_idx]
lineage.speciation_completion_time = current_time
lineage_data[phase_idx]["species_id"] += 1
lineage.species_id = lineage_data[phase_idx]["species_id"]
orthospecies_lineages.append(lineage)
del incipient_species_lineages[lineage_idx]
elif event_type_idx == 4:
# Extinction of an incipient_species lineage
lineage_idx = self.rng.randint(0, len(incipient_species_lineages)-1)
incipient_species_lineages[lineage_idx].extinction_time = current_time
del incipient_species_lineages[lineage_idx]
else:
raise Exception("Unexpected event type index: {}".format(event_type_idx))
def _run_protracted_speciation_process(self, **kwargs):
self.reset()
max_time = kwargs.get("max_time", None)
max_extant_protracted_speciation_lineages = kwargs.get("max_extant_protracted_speciation_lineages", None)
max_full_species = kwargs.get("max_full_species", None)
is_correlate_protracted_speciation_and_full_speciation_trees = kwargs.get("is_correlate_protracted_speciation_and_full_speciation_trees", False)
taxon_namespace = kwargs.get("taxon_namespace", None)
is_full_species = not kwargs.get("is_initial_species_incipient", False)
if is_full_species:
initial_lineage = self._new_lineage(parent_lineage=None, is_full_species=True)
else:
initial_lineage = self._new_lineage(parent_lineage=None, is_full_species=False)
seed_node = self._new_node(lineage=initial_lineage)
protracted_speciation_tree = self.tree_factory( taxon_namespace=taxon_namespace, seed_node=seed_node)
protracted_speciation_tree.is_rooted = True
while True:
## Draw time to next event
event_rates = []
num_full_species = len(self.current_full_species_lineages)
if max_full_species is not None:
## note: expensive operation to count leaves!
try:
full_species_tree = self._assemble_full_species_tree(taxon_namespace=taxon_namespace)
num_leaves = len(full_species_tree.leaf_nodes())
if num_leaves >= max_full_species:
return self._postprocess_psm_and_full_species_trees(
full_species_tree=full_species_tree,
protracted_speciation_tree=protracted_speciation_tree,
is_correlate_protracted_speciation_and_full_speciation_trees=is_correlate_protracted_speciation_and_full_speciation_trees,
)
except ProtractedSpeciationModel.ProcessFailedException:
pass
num_incipient_species = len(self.current_incipient_species_lineages)
if max_extant_protracted_speciation_lineages is not None and (num_incipient_species + num_full_species) >= max_extant_protracted_speciation_lineages:
break
# Event type 0
event_rates.append(self.full_species_birth_rate * num_full_species)
# Event type 1
event_rates.append(self.full_species_extinction_rate * num_full_species)
# Event type 2
event_rates.append(self.incipient_species_birth_rate * num_incipient_species)
# Event type 3
event_rates.append(self.incipient_species_conversion_rate * num_incipient_species)
# Event type 4
event_rates.append(self.incipient_species_extinction_rate * num_incipient_species)
# All events
rate_of_any_event = sum(event_rates)
# Waiting time
waiting_time = self.rng.expovariate(rate_of_any_event)
if max_time and (self.current_time + waiting_time) > max_time:
t = max_time - self.current_time
for lineage in itertools.chain(self.current_full_species_lineages, self.current_incipient_species_lineages):
lineage.node.edge.length += t
self.current_time = max_time
break
self.current_time += waiting_time
for lineage in itertools.chain(self.current_full_species_lineages, self.current_incipient_species_lineages):
lineage.node.edge.length += waiting_time
# Select event
event_type_idx = probability.weighted_index_choice(weights=event_rates, rng=self.rng)
assert (event_type_idx >= 0 and event_type_idx <= 4)
# print("time {}: {}, selected = {}".format(self.current_time, event_rates, event_type_idx))
if event_type_idx == 0:
self._process_full_species_birth(protracted_speciation_tree)
elif event_type_idx == 1:
self._process_full_species_extinction(protracted_speciation_tree)
elif event_type_idx == 2:
self._process_incipient_species_birth(protracted_speciation_tree)
elif event_type_idx == 3:
self._process_incipient_species_conversion(protracted_speciation_tree)
elif event_type_idx == 4:
self._process_incipient_species_extinction(protracted_speciation_tree)
else:
raise Exception("Unexpected event type index: {}".format(event_type_idx))
if len(self.current_full_species_lineages) + len(self.current_incipient_species_lineages) == 0:
raise TreeSimTotalExtinctionException()
full_species_tree = self._assemble_full_species_tree(taxon_namespace=taxon_namespace)
return self._postprocess_psm_and_full_species_trees(
protracted_speciation_tree=protracted_speciation_tree,
full_species_tree=full_species_tree,
is_correlate_protracted_speciation_and_full_speciation_trees=is_correlate_protracted_speciation_and_full_speciation_trees,
)
def _run_protracted_speciation_process(self, **kwargs):
self.reset()
max_time = kwargs.get("max_time", None)
max_extant_lineages = kwargs.get("max_extant_lineages", None)
max_extant_orthospecies = kwargs.get("max_extant_orthospecies", None)
is_correlate_lineage_and_species_trees = kwargs.get(
"is_correlate_lineage_and_species_trees", False)
taxon_namespace = kwargs.get("taxon_namespace", None)
initial_lineage = self._new_lineage(
parent_lineage=None,
orthospecies_index=self.current_orthospecies_index,
is_orthospecies=kwargs.get("is_initial_lineage_orthospecies",
True),
)
seed_node = self._new_node(lineage=initial_lineage)
lineage_tree = self.tree_factory(taxon_namespace=taxon_namespace,
seed_node=seed_node)
lineage_tree.is_rooted = True
while True:
## Draw time to next event
event_rates = []
num_orthospecies = len(self.current_orthospecies_lineages)
if max_extant_orthospecies is not None:
## note: expensive operation to count leaves!
try:
orthospecies_tree = self._assemble_orthospecies_tree(
taxon_namespace=taxon_namespace)
num_leaves = len(orthospecies_tree.leaf_nodes())
if num_leaves >= max_extant_orthospecies:
return self._postprocess_psm_and_orthospecies_trees(
orthospecies_tree=orthospecies_tree,
lineage_tree=lineage_tree,
is_correlate_lineage_and_species_trees=
is_correlate_lineage_and_species_trees,
)
except ProcessFailedException:
pass
num_incipient_species = len(
self.current_incipient_species_lineages)
if max_extant_lineages is not None and (
num_incipient_species +
num_orthospecies) >= max_extant_lineages:
break
# Event type 0
event_rates.append(
self.speciation_initiation_from_orthospecies_rate *
num_orthospecies)
# Event type 1
event_rates.append(self.orthospecies_extinction_rate *
num_orthospecies)
# Event type 2
event_rates.append(
self.speciation_initiation_from_incipient_species_rate *
num_incipient_species)
# Event type 3
event_rates.append(self.speciation_completion_rate *
num_incipient_species)
# Event type 4
event_rates.append(self.incipient_species_extinction_rate *
num_incipient_species)
# All events
rate_of_any_event = sum(event_rates)
# Waiting time
waiting_time = self.rng.expovariate(rate_of_any_event)
if max_time and (self.current_time + waiting_time) > max_time:
t = max_time - self.current_time
for lineage in itertools.chain(
self.current_orthospecies_lineages,
self.current_incipient_species_lineages):
lineage.node.edge.length += t
self.current_time = max_time
break
self.current_time += waiting_time
for lineage in itertools.chain(
self.current_orthospecies_lineages,
self.current_incipient_species_lineages):
lineage.node.edge.length += waiting_time
# Select event
event_type_idx = probability.weighted_index_choice(
weights=event_rates, rng=self.rng)
assert (event_type_idx >= 0 and event_type_idx <= 4)
# print("time {}: {}, selected = {}".format(self.current_time, event_rates, event_type_idx))
if event_type_idx == 0:
self._process_initiation_of_speciation_from_orthospecies(
lineage_tree)
elif event_type_idx == 1:
self._process_orthospecies_extinction(lineage_tree)
elif event_type_idx == 2:
self._process_initiation_of_speciation_from_incipient_species(
lineage_tree)
elif event_type_idx == 3:
self._process_completion_of_specation(lineage_tree)
elif event_type_idx == 4:
self._process_incipient_species_extinction(lineage_tree)
else:
raise Exception(
"Unexpected event type index: {}".format(event_type_idx))
if len(self.current_orthospecies_lineages) + len(
self.current_incipient_species_lineages) == 0:
raise TreeSimTotalExtinctionException()
orthospecies_tree = self._assemble_orthospecies_tree(
taxon_namespace=taxon_namespace)
return self._postprocess_psm_and_orthospecies_trees(
lineage_tree=lineage_tree,
orthospecies_tree=orthospecies_tree,
is_correlate_lineage_and_species_trees=
is_correlate_lineage_and_species_trees,
)