Jumps are encoded as jump from row-index to column-index, i.e.
C[1,2] == 10 means 10 jumps from state 1 to state 2, while
C[2,1] == 20 means 20 jumps from state 2 to state 1.
msm.countMatrix(traj, lag)
Arguments
traj
State trajectory, either encoded as vector or a filename.
lag
time lag to use for counting jumps: traj[i] -> traj[i+lag].