population-structure 1.0.1

Major changes in the the utils module. The f_to_m function previously used a numeric solver which oftenfailed due to constraining the solution with conservative migration constraints. Now, using the constraintsthe numerical solver adds the constraints as part of the equations to minimize, and it possible to runthe function without the conservative migration constraints.

Population Structure Package

A package for performing transformation between fst, coalescence, and migration matrices. The transformation between coalescence and migration is based on Wilkinson-Herbot's equations (2003). The transformation between fst and coalescence is based on the Slatkin's equations (1991).

Install package using pip

pip install population-structure

Example usuage

import population_structure.utils as psu
import numpy as np
m = np.array([[0, 1, 1], 
              [1, 0, 1], 
              [1, 1, 0]]) # A conservative migration matrix
t = psu.m_to_t(m) # The corresponding coalescence matrix according to W.H. (2003)
f = psu.m_to_f(m) # The corresponding fst matrix according to Slatkin (1991)
print(f"{t}\n{f}")
"""
prints:
[[3. 4. 4.]
 [4. 3. 4.]
 [4. 4. 3.]]
[[0.         0.14285714 0.14285714]
 [0.14285714 0.         0.14285714]
 [0.14285714 0.14285714 0.        ]]
"""
f = np.array([[0,0.1,0.2],
              [0.1,0,0.3],
              [0.2,0.3,0]]) # An fst matrix
psu.f_to_t(f) # Generates a possilbe corresponding coalescence matrix
psu.f_to_m(f) # Generate a possible corresponding migration matrix