exptheta : array
The element-wise exponential of the free parameters, theta.
These values are the linearized elements of the upper triangular portion
of the symmetric rate matrix, S, followed by the equilibrium weights.
n : int
Dimension of the rate matrix, K, (number of states)
u : int
The index, 0 <= u < len(exptheta) of the element in theta to
construct the derivative of the rate matrix, K with respect to.
inds : array, optional (default=None)
Sparse linearized triu indices exptheta. If not supplied, exptheta is
assumed to be a dense parameterization of the upper triangular portion
of the symmetric rate matrix followed by the log equilibrium weights,
and must be of length n*(n-1)/2 + n. If inds is supplied, it is a
set of indices, with len(inds) == len(exptheta),
0 <= inds < n*(n-1)/2+n, giving the indices of the nonzero elements
of the upper triangular elements of the rate matrix to which
exptheta correspond.
A : array of shape=(n, n), optional
If not None, an arbitrary (n, n) matrix to be multiplied element-wise
with the derivative of the rate matrix, dKu.
out : [output], optional array of shape=(n, n)
If not None, out will contain the matrix dKu on exit.
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