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A list giving information about the structure of states and allowed transitions in a multi-state model, and options for likelihood calculation. Used in internal computations, and returned in a fitted msm model object.



Number of states


Label for which basic structure the model is isomorphic to in the list of structures for which analytic formulae for the transition probabilities are implemented in the source file src/analyticp.c. This list is given by the internal object msm:::.msm.graphs which is defined and documented in the source file R/constants.R.

iso is 0 if the analytic P matrix is not implemented for this structure, or if analytic P matrix calculations are disabled using use.analyticp=FALSE in the call to msm.


Permutation required to convert the base isomorphism into the structure of this model. A vector of integers whose \(r\)th element is the state number in the base structure representing state \(r\) in the current structure.


Inverse permutation: vector whose \(r\)th element is the state number in the current structure representing the \(r\)th state in the base structure.


Number of allowed instantaneous transitions, equal to sum(imatrix).


Indicator matrix for allowed instantaneous transitions. This has \((r,s)\) entry 1 if the transition from \(r\) to \(s\) is permitted in continuous time, and 0 otherwise. The diagonal entries are arbitrarily set to 0.


Matrix of initial values for the transition intensities, supplied as the qmatrix 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 intensities, taken from the qconstraint argument to msm, and mapped if necessary to the set (1,2,3,...).


Number of distinct allowed instantaneous transitions, after applying equality constraints.


Use expm package to calculate matrix exponentials for likelihoods, as supplied to the use.expm argument of msm. TRUE or FALSE.