Number of states (same as qmodel$nstates).

Number of allowed misclassifications, equal to sum(imatrix).

Indicator matrix for allowed misclassifications. This has (r,s) entry 1 if misclassification of true state r as observed state s is possible. diagonal entries are arbitrarily set to 0.

Matrix of initial values for the misclassification probabilities, supplied as the ematrix argument of msm.

Vector of these initial values, reading across rows of qmatrix and excluding the diagonal and disallowed transitions.

Indicators for equality constraints on baseline misclassification probabilities, taken from the econstraint argument to msm, and mapped if necessary to the set (1,2,3,...)

Number of distinct misclassification probabilities, after applying equality constraints.

Number of initial state occupancy probabilities being estimated. This is zero if est.initprobs=FALSE, otherwise equal to the number of states.

Initial state occupancy probabilities, as supplied to msm (initial values before estimation, if est.initprobs=TRUE.)

Are initial state occupancy probabilities estimated (TRUE or FALSE), as supplied in the est.initprobs argument of msm.