Developer documentation: transition model structure object

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.

Value

nstates

Number of states

iso

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.

perm

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.

qperm

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

npars

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

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.

qmatrix

Matrix of initial values for the transition intensities, supplied as the qmatrix argument of msm.

inits

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

constr

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

ndpars

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

expm

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

See also

msm.object,emodel.object, hmodel.object.