secsse (version 3.0.2)

create_q_matrix: 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
)

Value

transition matrix

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:

1. starting state (typically the column in the transition matrix)

2. ending state (typically the row in the transition matrix)

3. 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.

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)