msmbuilder.msm._ratematrix.sigma_timescales¶

msmbuilder.msm._ratematrix.sigma_timescales()¶

sigma_timescales(covar_theta, theta, n):

Estimate the asymptotic standard deviation (uncertainty) in the implied timescales.

Parameters:

covar_theta : array, shape=(len(theta), len(theta)) Covariance matrix of theta. This is estimated by the inverse hessian of the log likelihood function. theta : array of shape = (n*(n-1)/2 + n) The free parameters of the model at the MLE. These values are the linearized elements of the upper triangular portion of the symmetric rate matrix, S, followed by the log of the equilibrium distribution. n : int The size of counts

Returns:

sigma_t : array, shape=(n-1,) Estimate of the element-wise asymptotic standard deviation of the relaxation timescales of the model.