msmbuilder.MSMLib.build_msm

msmbuilder.MSMLib.build_msm(counts, symmetrize='MLE', ergodic_trimming=True)

Estimates the transition probability matrix from the counts matrix.

Parameters:

counts : 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