Commit b17bc6fb authored by Ryan Gutenkunst's avatar Ryan Gutenkunst
Browse files

Add filter_pos method to PhiManip

parent 6f98a81a
......@@ -885,6 +885,23 @@ def remove_pop(phi, xx, popnum):
return Numerics.trapz(phi, xx, axis=popnum-1)
def filter_pops(phi, xx, tokeep):
Filter phi to keep only certain populations.
Returns new phi with len(tokeep) fewer populations.
phi: phi corresponding to original populations
xx: Mapping of points in phi to frequencies in population to be removed
tokeep: List of population numbers to keep, numbering from 1.
toremove = list(range(1, phi.ndim+1))
for pop_ii in tokeep:
for pop_ii in sorted(toremove)[::-1]:
phi = remove_pop(phi, xx, pop_ii)
return phi
def phi_1D_X(xx, nu=1.0, theta0=1.0, gamma=0, h=0.5, beta=1, alpha=1):
One-dimensional phi for a constant-sized population with genic selection.
import unittest
import numpy as np
import dadi
class PhiManipTestCase(unittest.TestCase):
def test_filter_pops(self):
Test filtering of populations
pts = 5
nu1,nu2,nu3,T = 0.1, 1, 10, 0.1
# Compare phi's from this 3D integration
xx = dadi.Numerics.default_grid(pts)
phi = dadi.PhiManip.phi_1D(xx)
phi = dadi.PhiManip.phi_1D_to_2D(xx, phi)
phi = dadi.PhiManip.phi_2D_to_3D(phi, 0, xx,xx,xx)
phi_all = dadi.Integration.three_pops(phi, xx, T=T, nu1=nu1, nu2=nu2, nu3=nu3)
phi = dadi.PhiManip.phi_1D(xx)
phi1 = dadi.Integration.one_pop(phi, xx, T=T, nu=nu1)
phi = dadi.PhiManip.phi_1D(xx)
phi2 = dadi.Integration.one_pop(phi, xx, T=T, nu=nu2)
# Note that we can't directly compare with nu3=10, because it will have different
# timesteps in integration, leading to different results. Here we fix timesteps
# by doing a 2D integration.
phi = dadi.PhiManip.phi_1D(xx)
phi = dadi.PhiManip.phi_1D_to_2D(xx, phi)
phi3 = dadi.Integration.two_pops(phi, xx, T=T, nu1=nu1, nu2=nu3)
self.assertTrue(np.allclose(phi1[1:-1], dadi.PhiManip.filter_pops(phi_all, xx, [1])[1:-1]))
self.assertTrue(np.allclose(phi2[1:-1], dadi.PhiManip.filter_pops(phi_all, xx, [2])[1:-1]))
phi3_comp = dadi.PhiManip.filter_pops(phi_all, xx, [1,3])
phi3[0,0] = phi3[-1,-1] = phi3_comp[0,0] = phi3_comp[-1,-1] = 0
self.assertTrue(np.allclose(phi3, phi3_comp))
suite = unittest.TestLoader().loadTestsFromTestCase(PhiManipTestCase)
if __name__ == '__main__':
\ No newline at end of file
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