def test_2d_freeze_marginal(self):
"""
Test marginal spectra from 2d freezing
"""
xx = dadi.Numerics.default_grid(30)
phi = dadi.PhiManip.phi_1D(xx)
phi_orig = dadi.PhiManip.phi_1D_to_2D(xx, phi)
phi_frozen1 = two_pops(phi_orig,
xx,
T=0.1,
nu2=0.3,
gamma2=0.5,
frozen1=True)
phi_frozen2 = two_pops(phi_orig,
xx,
T=0.1,
nu1=0.2,
gamma1=0.3,
frozen2=True)
phi_decouple = two_pops(phi_orig,
xx,
T=0.1,
nu1=0.2,
gamma1=0.3,
nu2=0.3,
gamma2=0.5)
phi_orig_just1 = dadi.PhiManip.remove_pop(phi_orig, xx, 2)
phi_orig_just2 = dadi.PhiManip.remove_pop(phi_orig, xx, 1)
phi_frozen1_just1 = dadi.PhiManip.remove_pop(phi_frozen1, xx, 2)
phi_frozen1_just2 = dadi.PhiManip.remove_pop(phi_frozen1, xx, 1)
phi_frozen2_just1 = dadi.PhiManip.remove_pop(phi_frozen2, xx, 2)
phi_frozen2_just2 = dadi.PhiManip.remove_pop(phi_frozen2, xx, 1)
phi_decouple_just1 = dadi.PhiManip.remove_pop(phi_decouple, xx, 2)
phi_decouple_just2 = dadi.PhiManip.remove_pop(phi_decouple, xx, 1)
# Checks that if I freeze a population, the marginal spectrum
# for that population does not change during integration.
self.assert_(
numpy.allclose(phi_orig_just1[1:-1],
phi_frozen1_just1[1:-1],
rtol=1e-4))
self.assert_(
numpy.allclose(phi_orig_just2[1:-1],
phi_frozen2_just2[1:-1],
rtol=1e-4))
# Checks that if I freeze a population, the other population
# continues to evolve as if decoupled from frozen population.
# These tests are much less precise than those above, becaue
# my integration scheme doesn't explicitly decouple the populations.
self.assert_(
numpy.allclose(phi_frozen2_just1[1:-1],
phi_decouple_just1[1:-1],
rtol=5e-2))
self.assert_(
numpy.allclose(phi_frozen1_just2[1:-1],
phi_decouple_just2[1:-1],
rtol=5e-2))
def test_2d_freeze_marginal(self):
"""
Test marginal spectra from 2d freezing
"""
xx = dadi.Numerics.default_grid(30)
phi = dadi.PhiManip.phi_1D(xx)
phi = one_pop(phi, xx, T=0.2, nu=0.1)
phi_orig = dadi.PhiManip.phi_1D_to_2D(xx, phi)
phi_frozen1 = two_pops(phi_orig, xx, T=0.1, nu2=0.3, gamma2=0.5,
frozen1=True)
phi_frozen2 = two_pops(phi_orig, xx, T=0.1, nu1=0.2, gamma1=0.3,
frozen2=True)
phi_decouple = two_pops(phi_orig, xx, T=0.1, nu1=0.2, gamma1=0.3,
nu2=0.3, gamma2=0.5)
phi_orig_just1 = dadi.PhiManip.remove_pop(phi_orig, xx, 2)
phi_orig_just2 = dadi.PhiManip.remove_pop(phi_orig, xx, 1)
phi_frozen1_just1 = dadi.PhiManip.remove_pop(phi_frozen1, xx, 2)
phi_frozen1_just2 = dadi.PhiManip.remove_pop(phi_frozen1, xx, 1)
phi_frozen2_just1 = dadi.PhiManip.remove_pop(phi_frozen2, xx, 2)
phi_frozen2_just2 = dadi.PhiManip.remove_pop(phi_frozen2, xx, 1)
phi_decouple_just1 = dadi.PhiManip.remove_pop(phi_decouple, xx, 2)
phi_decouple_just2 = dadi.PhiManip.remove_pop(phi_decouple, xx, 1)
# Checks that if I freeze a population, the marginal spectrum
# for that population does not change during integration.
self.assert_(numpy.allclose(phi_orig_just1[1:-1],
phi_frozen1_just1[1:-1],
rtol=1e-4))
self.assert_(numpy.allclose(phi_orig_just2[1:-1],
phi_frozen2_just2[1:-1],
rtol=1e-4))
# Checks that if I freeze a population, the other population
# continues to evolve as if decoupled from frozen population.
# These tests are much less precise than those above, becaue
# my integration scheme doesn't explicitly decouple the populations.
self.assert_(numpy.allclose(phi_frozen2_just1[1:-1],
phi_decouple_just1[1:-1],
rtol=5e-2))
self.assert_(numpy.allclose(phi_frozen1_just2[1:-1],
phi_decouple_just2[1:-1],
rtol=5e-2))
def test_2d_correctness(self):
"""
Test marginal spectra from 3d freezing
"""
xx = dadi.Numerics.default_grid(30)
phi = dadi.PhiManip.phi_1D(xx)
phi = dadi.PhiManip.phi_1D_to_2D(xx, phi)
phi = two_pops(phi, xx, T=0.1, nu2=0.3, gamma2=0.5, frozen1=True)
fs = dadi.Spectrum.from_phi(phi, [10,10], [xx,xx])
fs_stored = dadi.Spectrum.from_file('test_2D_frozen1.fs')
self.assert_(numpy.ma.allclose(fs, fs_stored, rtol=1e-2))
def test_2d_correctness(self):
"""
Test marginal spectra from 3d freezing
"""
xx = dadi.Numerics.default_grid(30)
phi = dadi.PhiManip.phi_1D(xx)
phi = dadi.PhiManip.phi_1D_to_2D(xx, phi)
phi = two_pops(phi, xx, T=0.1, nu2=0.3, gamma2=0.5, frozen1=True)
fs = dadi.Spectrum.from_phi(phi, [10, 10], [xx, xx])
fs_stored = dadi.Spectrum.from_file('test_2D_frozen1.fs')
self.assert_(numpy.ma.allclose(fs, fs_stored, rtol=1e-2))
