def build_ctmc_system(self, isolation_time, migration_time, coal_rate,
recomb_rate, mig_rate):
"""Construct CTMCs and compute HMM matrices given the split times
and the rates."""
# We assume here that the coalescence rate is the same in the two
# separate populations as it is in the ancestral. This is not necessarily
# true but it worked okay in simulations in Mailund et al. (2012).
isolation_rates = make_rates_table_isolation(coal_rate, coal_rate,
recomb_rate)
isolation_ctmc = make_ctmc(self.isolation_state_space, isolation_rates)
migration_rates = make_rates_table_migration(coal_rate, coal_rate,
recomb_rate, mig_rate,
mig_rate)
migration_ctmc = make_ctmc(self.migration_state_space, migration_rates)
single_rates = make_rates_table_single(coal_rate, recomb_rate)
single_ctmc = make_ctmc(self.single_state_space, single_rates)
tau1 = isolation_time
tau2 = isolation_time + migration_time
migration_break_points = uniform_break_points(self.no_mig_states, tau1,
tau2)
ancestral_break_points = exp_break_points(self.no_ancestral_states,
coal_rate, tau2)
return IsolationMigrationCTMCSystem(isolation_ctmc, migration_ctmc,
single_ctmc,
migration_break_points,
ancestral_break_points)
def build_ctmc_system(self, *parameters):
"""Construct CTMCs and compute HMM matrices given the split times
and the rates."""
isolation_time, migration_time, recomb_rate = parameters[:3]
coal_rates = parameters[3:2 * self.no_epochs + 1 + 3]
mig_rates = parameters[2 * self.no_epochs + 1 + 3:]
assert len(
coal_rates
) == self.no_epochs * 2 + 1, "Isolation + #Epochs migration + #Epochs ancestral"
assert len(mig_rates) == self.no_epochs, "#Epochs migration epochs"
isolation_rates = make_rates_table_isolation(coal_rates[0],
coal_rates[0],
recomb_rate)
isolation_ctmc = make_ctmc(self.isolation_state_space, isolation_rates)
migration_ctmcs = []
ancestral_ctmcs = []
for epoch in xrange(self.no_epochs):
migration_rates = make_rates_table_migration(
coal_rates[epoch + 1], coal_rates[epoch + 1], recomb_rate,
mig_rates[epoch], mig_rates[epoch])
migration_ctmc = make_ctmc(self.migration_state_space,
migration_rates)
# Repeat of the same CTMC throughout the epoch. Change here if different number of states per epoch
for _ in xrange(self.no_mig_states):
migration_ctmcs.append(migration_ctmc)
for epoch in xrange(self.no_epochs):
ancestral_rates = make_rates_table_single(
coal_rates[epoch + self.no_epochs + 1], recomb_rate)
ancestral_ctmc = make_ctmc(self.single_state_space,
ancestral_rates)
# Repeat of the same CTMC throughout the epoch. Change here if different number of states per epoch
for _ in xrange(self.no_ancestral_states):
ancestral_ctmcs.append(ancestral_ctmc)
tau1 = isolation_time
tau2 = isolation_time + migration_time
migration_break_points = uniform_break_points(
self.no_epochs * self.no_mig_states, tau1, tau2)
# FIXME: This should take into account that the coal rate varies between epochs...
coal_rate = mean(coal_rates[self.no_epochs + 1:])
ancestral_break_points = exp_break_points(
self.no_epochs * self.no_ancestral_states, coal_rate, tau2)
return IsolationMigrationEpochsCTMCSystem(isolation_ctmc,
migration_ctmcs,
ancestral_ctmcs,
migration_break_points,
ancestral_break_points)
def build_ctmc_system(self, tau1, tau2, coal1, coal2, coal3, coal12, coal123, recombination_rate):
"""Construct CTMC system."""
epoch_1_ctmc = make_ctmc(Isolation3(), make_rates_table_3(coal1, coal2, coal3, recombination_rate))
epoch_2_ctmc = make_ctmc(Isolation2(), make_rates_table_2(coal12, coal3, recombination_rate))
epoch_3_ctmc = make_ctmc(Isolation1(), make_rates_table_1(coal123, recombination_rate))
self.break_points_12 = trunc_exp_break_points(self.no_12_intervals, coal12, tau1 + tau2, tau1)
self.break_points_123 = exp_break_points(self.no_123_intervals, coal123, tau1 + tau2)
return ILSCTMCSystem(self, epoch_1_ctmc, epoch_2_ctmc, epoch_3_ctmc, self.break_points_12, self.break_points_123)
def emission_points(self, isolation_time, migration_time, coal_rate,
recomb_rate, mig_rate):
"""Compute model specific coalescence points."""
tau1 = isolation_time
tau2 = isolation_time + migration_time
migration_break_points = uniform_break_points(self.no_mig_states, tau1,
tau2)
ancestral_break_points = exp_break_points(self.no_ancestral_states,
coal_rate, tau2)
break_points = list(migration_break_points) + list(
ancestral_break_points)
return coalescence_points(break_points, coal_rate)
def emission_points(self, *parameters):
"""Compute model specific coalescence points."""
isolation_time, migration_time, recomb_rate = parameters[:3]
coal_rates = parameters[3:2 * self.no_epochs + 1 + 3]
tau1 = isolation_time
tau2 = isolation_time + migration_time
migration_break_points = uniform_break_points(
self.no_epochs * self.no_mig_states, tau1, tau2)
# FIXME: This should really take into account that the coal rate varies between epochs...
coal_rate = mean(coal_rates)
ancestral_break_points = exp_break_points(
self.no_epochs * self.no_ancestral_states, coal_rate, tau2)
break_points = list(migration_break_points) + list(
ancestral_break_points)
return coalescence_points(break_points, coal_rate)
def get_ancestral_break_points(self, tau_1, tau_2, coal_a):
return exp_break_points(self.no_ancestral_states, coal_a,
tau_1 + tau_2)