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Returns a matrix with counts of transitions
Nij(CTMC)
(Fully observed) CTMC.
numeric matrix(ncol=max(CTMC)+1, nrow=max(CTMC)+1) where max(CTMC) is the max state of the CTMC.
the (i,j) element is the number of transitions from state (i-1) to state (j-1) that were observed.