create_default_shift_matrix: Helper function to create a default 'shift_matrix' list

In secsse: Several Examined and Concealed States-Dependent Speciation and Extinction

Helper function to create a default shift_matrix list

Description

This function generates a generic shift matrix to be used with the function create_q_matrix().

Usage

create_default_shift_matrix(
  state_names = c("0", "1"),
  num_concealed_states = 2,
  mu_vector = NULL
)

Arguments

state_names	vector of names of all observed states.
num_concealed_states	number of concealed states, generally equivalent to the number of examined states in the dataset.
mu_vector	previously defined mus - used to choose indicator number.

Examples

shift_matrix <- create_default_shift_matrix(state_names = c(0, 1),
                                            num_concealed_states = 2,
                                            mu_vector = c(1, 2, 1, 2))
q_matrix <- create_q_matrix(state_names = c(0, 1),
                            num_concealed_states = 2,
                            shift_matrix = shift_matrix,
                            diff.conceal = FALSE)

secsse documentation built on Oct. 22, 2023, 1:13 a.m.