theta : array
The free parameters, theta. These values are the linearized elements
of the upper triangular portion of the symmetric rate matrix, S,
followed by the log equilibrium weights.
n : int
Dimension of the rate matrix, K, (number of states)
which : {‘S’, ‘K’}
Whether to build the matrix S or the matrix K
out : [output], array shape=(n, n)
On exit, out contains the matrix K or S
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