Q.matr.setup.general {flexmsm}

Internal function

Description

Internal function needed for setup of Q matrix and its first and second derivative.

Usage

Q.matr.setup.general(
  params,
  nstates,
  full.X,
  start.pos.par,
  l.short.formula,
  whereQ,
  firstD = TRUE,
  secondD = TRUE,
  bound.eta = FALSE,
  pos.optparams,
  pos.optparams2
)

Arguments

params

Parameters vector.

nstates

Number of states.

full.X

Full design matrix.

start.pos.par

Positions within full parameters vector of starting point for each sub-parameters vector corresponding to each transition intensity specification.

l.short.formula

Number of transitions.

whereQ

Positions within Q matrix of not-null transition intensities.

firstD

Whether the first derivative of the Q matrix should be computed.

secondD

Whether the second derivative of the Q matrix should be computed.

bound.eta

Whether to bound the additive predictor, defaults to FALSE. This is only used for debugging purposes, do not change.

pos.optparams

Vector with positions of parameters vector in the form used by the optimization algorithm (i.e. when one or more parameters are constrained to be equal these will only appear once).

pos.optparams2

Like pos.optparams but the count is not stopped at the constrained parameters.

Value

Q matrix and its first and second derivatives with respect to the parameters vector.