Q.matr.setup.general function

Internal function

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

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.

Returns

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