def get_fixation_unconstrained_kb_fquad_cython(S, d, log_kb, mask):
"""
This uses the Kacser and Burns effect instead of the sign function.
"""
D = d * numpy.tanh(numpy.exp(log_kb) * S)
H = 1. / kimrecessive.denom_fixed_quad_cython(0.5*S, D, mask)
return H
def get_fixation_unconstrained_fquad_cython(S, d, mask):
"""
This is not compatible with algopy.
In this function name, fquad means "fixed quadrature."
The S ndarray with ndim=2 depends on free parameters.
The d parameter is itself a free parameter.
The mask specifies which codon pairs are mutational neighbors.
@param S: array of selection differences
@param d: parameter that controls dominance vs. recessivity
@param mask: only compute entries of neighboring codon pairs
"""
H = 1. / kimrecessive.denom_fixed_quad_cython(0.5*S, d*numpy.sign(S), mask)
return H
