Process and standardise formulas for the state process of hidden Markov models

Usage

process_hid_formulas(formulas, nStates, ref = NULL)

Arguments

formulas: formulas for the transition process of a hidden Markov model, either as a single formula, a list of formulas, or a matrix.
nStates: number of states of the Markov chain
ref: optional vector of reference categories for each state, defaults to 1:nStates. If provided, must be of length nStates and contain valid state indices. If a formula matrix is provided, this cannot be specified because reference categries are specified by one "." entry in each row.

Value

named list of formulas of length nStates * (nStates - 1), where each formula corresponds to a transition from state \(i\) to state \(j\), excluding transitions from i to ref[i].

Examples

# single formula for all non-reference category elements
formulas = process_hid_formulas(~ s(x), nStates = 3)
# now a list of length 6 with names tr.ij, not including reference categories

# different reference categories
formulas = process_hid_formulas(~ s(x), nStates = 3, ref = c(1,1,1))

# different formulas for different entries (and only for 2 of 6)
formulas = list(tr.12 ~ s(x), tr.23 ~ s(y))
formulas = process_hid_formulas(formulas, nStates = 3, ref = c(1,1,1))
# also a list of length 6, remaining entries filled with tr.ij ~ 1

# matrix input with reference categories
formulas = matrix(c(".", "~ s(x)", "~ s(y)",
                    "~ g", ".", "~ I(x^2)",
                    "~ y", "~ 1", "."), 
                    nrow = 3, byrow = TRUE)
# dots define reference categories
formulas = process_hid_formulas(formulas, nStates = 3)