msmbuilder.MSMLib.build_msm¶

msmbuilder.MSMLib.build_msm(counts, symmetrize='MLE', ergodic_trimming=True)[source]¶

Estimates the transition probability matrix from the counts matrix.

Parameters:	counts : scipy.sparse.csr_matrix the MSM counts matrix symmetrize : {‘MLE’, ‘Transpose’, None} symmetrization scheme so that we have reversible counts ergodic_trim : bool (optional) whether or not to trim states to achieve an ergodic model
Returns:	rev_counts : matrix the estimate of the reversible counts t_matrix : matrix the transition probability matrix populations : ndarray, float the equilibrium populations of each state mapping : ndarray, int a mapping from the passed counts matrix to the new counts and transition matrices