qmodel.object: Developer documentation: transition model structure object
Description
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
- nstatesNumber of states
- isoLabel 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. - permPermutation 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.
- qpermInverse permutation: vector whose $r$th element
is the state number in the current structure representing the
$r$th state in the base structure.
- nparsNumber of allowed instantaneous transitions, equal to
sum(imatrix). - imatrixIndicator 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.
- qmatrixMatrix of initial values for the transition
intensities, supplied as the
qmatrix argument of msm. - initsVector of these initial values, reading across rows of
qmatrix and excluding the diagonal and disallowed transitions. - constrIndicators for equality constraints on baseline
intensities, taken from the
qconstraint argument to
msm, and mapped if necessary to the set (1,2,3,...). - ndparsNumber of distinct allowed instantaneous transitions, after applying
equality constraints.
- expmUse expm package to calculate matrix exponentials
for likelihoods, as supplied to the
use.expm argument of
msm. TRUE or FALSE.