create_q_matrix: Helper function to neatly setup a Q matrix, without...

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

Helper function to neatly setup a Q matrix, without transitions to concealed states (only observed transitions shown)

Description

Helper function to neatly setup a Q matrix, without transitions to concealed states (only observed transitions shown)

Usage

create_q_matrix(
  state_names,
  num_concealed_states,
  shift_matrix,
  diff.conceal = FALSE
)

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.
shift_matrix	matrix of shifts, indicating in order: starting state (typically the column in the transition matrix) ending state (typically the row in the transition matrix) associated rate indicator.
diff.conceal	Boolean stating if the concealed states should be different. E.g. that the transition rates for the concealed states are different from the transition rates for the examined states. Normally it should be FALSE in order to avoid having a huge number of parameters.

Value

transition matrix

Examples

shift_matrix <- c(0, 1, 5)
shift_matrix <- rbind(shift_matrix, c(1, 0, 6))
q_matrix <- secsse::create_q_matrix(state_names = c(0, 1),
                                    num_concealed_states = 2,
                                    shift_matrix = shift_matrix,
                                    diff.conceal = TRUE)

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