Generate Transition and Initial Probabilities

Generate random transition probabilities and initial state probabilities for a Markov chain using the seqHMM package.

Usage

generate_probabilities(
  n_states = 8,
  states = NULL,
  alpha = 1,
  diag_c = 0,
  seed = NULL,
  possible_state_names = NULL
)

Arguments

n_states

Integer. Number of states in the Markov chain. Default: 5.

states

Character vector. Names for the states. Must have at least n_states elements. If NULL, uses letters A, B, C, ... Default: NULL.

alpha

Numeric. Dirichlet concentration parameter passed to seqHMM::simulate_initial_probs() and seqHMM::simulate_transition_probs(). Small values (e.g., 0.1) produce sparse matrices with a few dominant transitions; large values (e.g., 10) produce near-uniform matrices. Default: 1.

diag_c

Numeric. Diagonal boost added before row normalisation, passed to seqHMM::simulate_transition_probs(). Higher values create "sticky" states with strong self-transitions. Default: 0.

seed

Integer or NULL. Random seed for reproducibility. Default: NULL.

possible_state_names

Deprecated. Use states instead.

Value

A list containing:

initial_probs

Named numeric vector of initial state probabilities.

transition_probs

Square matrix of transition probabilities with row and column names set to state names.

state_names

Character vector of state names used.

Details

The transition probabilities are generated using seqHMM::simulate_transition_probs() and initial probabilities using seqHMM::simulate_initial_probs().

Examples

if (FALSE) { # \dontrun{
# Generate probabilities for 4 states with default names
probs <- generate_probabilities(n_states = 4, seed = 42)

# Generate probabilities with custom state names
probs <- generate_probabilities(
  n_states = 4,
  states = c("A", "B", "C", "D", "E"),
  seed = 123
)

# View initial probabilities
probs$initial_probs

# View transition matrix
probs$transition_probs

# Old parameter name still works
probs <- generate_probabilities(
  n_states = 3,
  possible_state_names = c("X", "Y", "Z")
)
} # }